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ljmartin/rcsb_past_week.ipynb

Created October 27, 2020 23:34
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gistfile1.txt
{
"cells": [
{
"cell_type": "code",
"execution_count": 1,
"metadata": {},
"outputs": [],
"source": [
"import json\n",
"import urllib\n",
"from urllib.request import urlopen\n",
"import requests"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# Pinging rcsb for recent PDB uploads\n",
"\n",
"First use the RCSB search API to search for all entries uploaded in the previous week. Previous week is defined easily using `from: now-1w` and `to: now`"
]
},
{
"cell_type": "code",
"execution_count": 2,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"dict_keys(['query_id', 'result_type', 'total_count', 'explain_meta_data', 'result_set'])\n"
]
}
],
"source": [
"url = 'https://search.rcsb.org/rcsbsearch/v1/query'\n",
"\n",
"json_query_string = \"\"\"\n",
"{\n",
" \"query\": {\n",
" \"type\": \"terminal\",\n",
" \"service\": \"text\",\n",
" \"parameters\": {\n",
" \"attribute\": \"rcsb_accession_info.initial_release_date\",\n",
" \"operator\": \"range\",\n",
" \"value\": {\n",
" \"from\": \"now-1w\",\n",
" \"to\": \"now\"\n",
" }\n",
" }\n",
" },\n",
" \"request_options\": {\n",
" \"return_all_hits\": true\n",
" },\n",
" \"return_type\": \"entry\"\n",
"}\n",
"\"\"\"\n",
"\n",
"query = urllib.parse.quote(json_query_string)\n",
"req_url = url+'?json={request}'\n",
"\n",
"url_query = req_url.format(request=query)\n",
"\n",
"response = urlopen(url_query)\n",
"out = json.loads(response.read())\n",
"print(out.keys())"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# GraphQL query to retrieve PDB titles\n",
"\n",
"The above is limited to returning PDB codes. To get further information about these, construct a graphql query using all those codes"
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"\n"
]
}
],
"source": [
"#get the pdb codes, labelled 'identifier':\n",
"pdb_codes = [i['identifier'] for i in out['result_set']]\n",
"print()"
]
},
{
"cell_type": "code",
"execution_count": 4,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"{'data': {'entries': [{'rcsb_id': '6TI9',\n",
" 'struct': {'title': 'Human transthyretin (TTR) complexed with (E)-3-(((3,5-dibromo-2-hydroxybenzylidene)amino)oxy)propanoic acid.'}},\n",
" {'rcsb_id': '6VKV',\n",
" 'struct': {'title': 'Co-crystal structure of GS-6207 bound to HIV-1 capsid hexamer'}},\n",
" {'rcsb_id': '6W1A',\n",
" 'struct': {'title': 'Crystal structure of Streptococcus dysgalactiae SHP pheromone receptor Rgg2 bound to DNA'}},\n",
" {'rcsb_id': '6W1E',\n",
" 'struct': {'title': 'Crystal structure of Streptococcus thermophilus SHP pheromone receptor Rgg3'}},\n",
" {'rcsb_id': '6W1F',\n",
" 'struct': {'title': 'Crystal structure of Streptococcus thermophilus SHP pheromone receptor Rgg3 bound to DNA'}},\n",
" {'rcsb_id': '6W4K',\n",
" 'struct': {'title': 'Crystal structure of Lysine Specific Demethylase 1 (LSD1) with CC-90011'}},\n",
" {'rcsb_id': '6W6K', 'struct': {'title': '30S-Activated-high-Mg2+'}},\n",
" {'rcsb_id': '6VW0',\n",
" 'struct': {'title': 'Mycobacterium tuberculosis RNAP S456L mutant open promoter complex'}},\n",
" {'rcsb_id': '6W7N', 'struct': {'title': '30S-Inactive-low-Mg2+ Class A'}},\n",
" {'rcsb_id': '6VVS',\n",
" 'struct': {'title': 'Crystal structure of a Mycobacterium smegmatis RNA polymerase transcription initiation complex with antibiotic Sorangicin'}},\n",
" {'rcsb_id': '6VVT',\n",
" 'struct': {'title': 'Crystal structure of a Mycobacterium smegmatis transcription initiation complex with Rifampicin-resistant RNA polymerase and antibiotic Sorangicin'}},\n",
" {'rcsb_id': '6W7M',\n",
" 'struct': {'title': '30S-Inactive-high-Mg2+ + carbon layer'}},\n",
" {'rcsb_id': '6W77',\n",
" 'struct': {'title': '30S-Inactivated-high-Mg2+ Class A'}},\n",
" {'rcsb_id': '6VWS',\n",
" 'struct': {'title': 'Hexamer of Helical HIV capsid by RASTR method'}},\n",
" {'rcsb_id': '6VWC',\n",
" 'struct': {'title': 'Crystal structure of Bcl-xL in complex with tetrahydroisoquinoline-pyridine based inhibitors'}},\n",
" {'rcsb_id': '6W7W', 'struct': {'title': '30S-Inactive-low-Mg2+ Class B'}},\n",
" {'rcsb_id': '6VVV',\n",
" 'struct': {'title': 'Crystal structure of a Mycobacterium smegmatis transcription initiation complex with Rifampicin-resistant RNA polymerase'}},\n",
" {'rcsb_id': '6W7V',\n",
" 'struct': {'title': 'Structure of rabbit actin in complex with truncated analog of Mycalolide B'}},\n",
" {'rcsb_id': '6VVY',\n",
" 'struct': {'title': 'Mycobacterium tuberculosis WT RNAP transcription open promoter complex with Sorangicin'}},\n",
" {'rcsb_id': '6VVX',\n",
" 'struct': {'title': 'Mycobacterium tuberculosis WT RNAP transcription initiation intermediate structure with Sorangicin'}},\n",
" {'rcsb_id': '6VVZ',\n",
" 'struct': {'title': 'Mycobacterium tuberculosis RNAP S456L mutant transcription initiation intermediate structure with Sorangicin'}},\n",
" {'rcsb_id': '6UW2',\n",
" 'struct': {'title': 'Clotrimazole bound complex of Acanthamoeba castellanii CYP51'}},\n",
" {'rcsb_id': '6UX0',\n",
" 'struct': {'title': 'Isavuconazole bound complex of Acanthamoeba castellanii CYP51'}},\n",
" {'rcsb_id': '6UZU',\n",
" 'struct': {'title': 'Carbonic Anhydrase IX-mimic In Complex WITH U-CH3'}},\n",
" {'rcsb_id': '6VAS',\n",
" 'struct': {'title': 'Assembly of VIQKI I454(beta-L-homoisoleucine)with human parainfluenza virus type 3 (HPIV3) fusion glycoprotein N-terminal heptad repeat domain'}},\n",
" {'rcsb_id': '6ZR2',\n",
" 'struct': {'title': 'Cryo-EM structure of respiratory complex I in the active state from Mus musculus at 3.1 A'}},\n",
" {'rcsb_id': '7K1W',\n",
" 'struct': {'title': 'PIKfyve/Fig4/Vac14 complex centered on Fig4 - map3'}},\n",
" {'rcsb_id': '7K1Y',\n",
" 'struct': {'title': 'PIKfyve/Fig4/Vac14 complex centered on Vac14 - map1'}},\n",
" {'rcsb_id': '6ZSA',\n",
" 'struct': {'title': 'Human mitochondrial ribosome bound to mRNA, A-site tRNA and P-site tRNA'}},\n",
" {'rcsb_id': '7K2V',\n",
" 'struct': {'title': 'PIKfyve/Fig4/Vac14 complex centered on PIKfyve - map2'}},\n",
" {'rcsb_id': '7K2U', 'struct': {'title': 'DHODH IN COMPLEX WITH LIGAND 13'}},\n",
" {'rcsb_id': '6ZTQ',\n",
" 'struct': {'title': 'Cryo-EM structure of respiratory complex I from Mus musculus inhibited by piericidin A at 3.0 A'}},\n",
" {'rcsb_id': '7JSN',\n",
" 'struct': {'title': 'Structure of the Visual Signaling Complex between Transducin and Phosphodiesterase 6'}},\n",
" {'rcsb_id': '7K74',\n",
" 'struct': {'title': 'Crystal Structure of Fructose-1,6-bisphosphatase, type I, from Stenotrophomonas maltophilia K279a'}},\n",
" {'rcsb_id': '7K8V',\n",
" 'struct': {'title': 'Structure of the SARS-CoV-2 S 2P trimer in complex with the human neutralizing antibody Fab fragment, C110'}},\n",
" {'rcsb_id': '7K8W',\n",
" 'struct': {'title': 'Structure of the SARS-CoV-2 S 2P trimer in complex with the human neutralizing antibody Fab fragment, C119'}},\n",
" {'rcsb_id': '7K8T',\n",
" 'struct': {'title': 'Structure of the SARS-CoV-2 S 2P trimer in complex with the human neutralizing antibody Fab fragment, C002 (state 1)'}},\n",
" {'rcsb_id': '7K8U',\n",
" 'struct': {'title': 'Structure of the SARS-CoV-2 S 2P trimer in complex with the human neutralizing antibody Fab fragment, C002 (state 1)'}},\n",
" {'rcsb_id': '7K8Z',\n",
" 'struct': {'title': 'Structure of the SARS-CoV-2 S 2P trimer in complex with the human neutralizing antibody Fab fragment, C135'}},\n",
" {'rcsb_id': '7K8X',\n",
" 'struct': {'title': 'Structure of the SARS-CoV-2 S 2P trimer in complex with the human neutralizing antibody Fab fragment, C121 (State 1)'}},\n",
" {'rcsb_id': '7K8Y',\n",
" 'struct': {'title': 'Structure of the SARS-CoV-2 S 2P trimer in complex with the human neutralizing antibody Fab fragment, C121 (State 2)'}},\n",
" {'rcsb_id': '7K8N',\n",
" 'struct': {'title': 'Crystal structure of an anti-SARS-CoV-2 human neutralizing antibody Fab fragment, C110'}},\n",
" {'rcsb_id': '7K8O',\n",
" 'struct': {'title': 'Crystal structure of an anti-SARS-CoV-2 human neutralizing antibody Fab fragment, C110'}},\n",
" {'rcsb_id': '7K90',\n",
" 'struct': {'title': 'Structure of the SARS-CoV-2 S 6P trimer in complex with the human neutralizing antibody Fab fragment, C144'}},\n",
" {'rcsb_id': '7K8M',\n",
" 'struct': {'title': 'Crystal structure of an anti-SARS-CoV-2 human neutralizing antibody Fab fragment, C110'}},\n",
" {'rcsb_id': '7K8R',\n",
" 'struct': {'title': 'Crystal structure of an anti-SARS-CoV-2 human neutralizing antibody Fab fragment, C135'}},\n",
" {'rcsb_id': '7K8S',\n",
" 'struct': {'title': 'Structure of the SARS-CoV-2 S 2P trimer in complex with the human neutralizing antibody Fab fragment, C002 (state 1)'}},\n",
" {'rcsb_id': '7K8P',\n",
" 'struct': {'title': 'Crystal structure of an anti-SARS-CoV-2 human neutralizing antibody Fab fragment, C110'}},\n",
" {'rcsb_id': '7K8Q',\n",
" 'struct': {'title': 'Crystal structure of an anti-SARS-CoV-2 human neutralizing antibody Fab fragment, C110'}},\n",
" {'rcsb_id': '7K9P',\n",
" 'struct': {'title': 'Room temperature structure of NSP15 Endoribonuclease from SARS CoV-2 solved using SFX.'}},\n",
" {'rcsb_id': '7JZT',\n",
" 'struct': {'title': 'Low resolution crystal structure of Zaire Ebola virus VP40 in space group P6422'}},\n",
" {'rcsb_id': '7KCP',\n",
" 'struct': {'title': \"Crystal structure of Acetyl-CoA Synthetase in Complex with Adenosine-5'-propylphosphate from Coccidioides posadasii C735\"}},\n",
" {'rcsb_id': '7C5D',\n",
" 'struct': {'title': 'Crystal structure of TRF2 TRFH domain in complex with a MCPH1 peptide'}},\n",
" {'rcsb_id': '7A1A',\n",
" 'struct': {'title': '2,3-Dihydroxybenzoate Decarboxylase of Aspergillus oryzae'}},\n",
" {'rcsb_id': '7A19',\n",
" 'struct': {'title': '2,3-Dihydroxybenzoate Decarboxylase of Aspergillus oryzae'}},\n",
" {'rcsb_id': '7KDT',\n",
" 'struct': {'title': 'Human Tom70 in complex with SARS CoV2 Orf9b'}},\n",
" {'rcsb_id': '7C6H',\n",
" 'struct': {'title': 'Crystal structure of beta-glycosides-binding protein (W177X) of ABC transporter in an open-liganded state bound to laminaribiose'}},\n",
" {'rcsb_id': '7C6G',\n",
" 'struct': {'title': 'Crystal structure of beta-glycosides-binding protein (W177X) of ABC transporter in an open-liganded state bound to gentiobiose'}},\n",
" {'rcsb_id': '7A29',\n",
" 'struct': {'title': 'Cryo-EM structure of the SARS-CoV-2 spike protein bound to neutralizing sybodies (Sb23) 2-up conformation'}},\n",
" {'rcsb_id': '7C67',\n",
" 'struct': {'title': 'Crystal structure of beta-glycosides-binding protein of ABC transporter in a closed state bound to cellotriose'}},\n",
" {'rcsb_id': '7KES',\n",
" 'struct': {'title': 'Crystal structure of meta-AAC0038, an environmental aminoglycoside resistance enzyme, mutant H168A in complex with apramycin and CoA'}},\n",
" {'rcsb_id': '7BTN',\n",
" 'struct': {'title': 'Crystal structure of human inorganic pyrophosphatase with metal ions'}},\n",
" {'rcsb_id': '7A69',\n",
" 'struct': {'title': 'Nanodisc reconstituted human ABCB1 in complex with MRK16 Fab and vincristine'}},\n",
" {'rcsb_id': '7A68',\n",
" 'struct': {'title': 'proteinase K crystallized from 0.5 M NaNO3'}},\n",
" {'rcsb_id': '7A5O', 'struct': {'title': 'Human MUC2 AAs 21-1397'}},\n",
" {'rcsb_id': '7A78',\n",
" 'struct': {'title': 'Crystal structure of RXR beta LBD in complexes with palmitic acid and GRIP-1 peptide'}},\n",
" {'rcsb_id': '7A77',\n",
" 'struct': {'title': 'Crystal structure of RXR alpha LBD in complexes with palmitic acid and GRIP-1 peptide'}},\n",
" {'rcsb_id': '7A79',\n",
" 'struct': {'title': 'Crystal structure of RXR gamma LBD in complexes with palmitic acid and GRIP-1 peptide'}},\n",
" {'rcsb_id': '7A9B',\n",
" 'struct': {'title': 'Crystal structure of Shank1 PDZ domain with ARAP3-derived peptide'}},\n",
" {'rcsb_id': '7A9U',\n",
" 'struct': {'title': 'N-TERMINAL BROMODOMAIN OF HUMAN BRD4 WITH 3-(3-(but-3-yn-1-yl)-3H-diazirin-3-yl)-N-(3-methyl-[1,2,4]triazolo[4,3-a]pyridin-8-yl)propanamide'}},\n",
" {'rcsb_id': '7CFT',\n",
" 'struct': {'title': 'Cryo-EM strucutre of human acid-sensing ion channel 1a in complex with snake toxin Mambalgin1 at pH 8.0'}},\n",
" {'rcsb_id': '7CFS',\n",
" 'struct': {'title': 'Cryo-EM strucutre of human acid-sensing ion channel 1a at pH 8.0'}},\n",
" {'rcsb_id': '7AEY',\n",
" 'struct': {'title': 'Salmonella typhimurium neuraminidase in complex with isocarba-DANA.'}},\n",
" {'rcsb_id': '7CM7',\n",
" 'struct': {'title': 'NAD+-bound Sarm1 E642A in the self-inhibited state'}},\n",
" {'rcsb_id': '7CM5',\n",
" 'struct': {'title': 'Full-length Sarm1 in a self-inhibited state'}},\n",
" {'rcsb_id': '7CM6',\n",
" 'struct': {'title': 'NAD+-bound Sarm1 in the self-inhibited state'}},\n",
" {'rcsb_id': '6PWM',\n",
" 'struct': {'title': 'ADC-7 in complex with Beta-lactam antibiotic ceftazidime'}},\n",
" {'rcsb_id': '6PWL',\n",
" 'struct': {'title': 'ADC-7 in complex with boronic acid transition state inhibitor LP06'}},\n",
" {'rcsb_id': '6QVX', 'struct': {'title': 'Escherichia coli DPS'}},\n",
" {'rcsb_id': '6JZO',\n",
" 'struct': {'title': 'Structure of the mouse TRPC4 ion channel'}},\n",
" {'rcsb_id': '6KF8',\n",
" 'struct': {'title': 'OsACBP2 in complex with C18:3-CoA'}},\n",
" {'rcsb_id': '6KMM',\n",
" 'struct': {'title': 'Crystal Structure of HEPES bound Dye Decolorizing peroxidase from Bacillus subtilis'}},\n",
" {'rcsb_id': '6KMN',\n",
" 'struct': {'title': 'Crystal Structure of Dye Decolorizing peroxidase from Bacillus subtilis'}},\n",
" {'rcsb_id': '6L4K',\n",
" 'struct': {'title': 'Human serum albumin-Palmitic acid-Cu compound'}},\n",
" {'rcsb_id': '6L4L',\n",
" 'struct': {'title': 'Crystal structure of S. aureus CntK in inactive state'}},\n",
" {'rcsb_id': '6LBG', 'struct': {'title': 'Structure of OR51B2 bound FEM1C'}},\n",
" {'rcsb_id': '6LBF', 'struct': {'title': 'Crystal structure of FEM1B'}},\n",
" {'rcsb_id': '6LBN', 'struct': {'title': 'Structure of SIL1-bound FEM1C'}},\n",
" {'rcsb_id': '6LEN', 'struct': {'title': 'Structure of NS11 bound FEM1C'}},\n",
" {'rcsb_id': '6LDP', 'struct': {'title': 'Structure of CDK5R1-bound FEM1C'}},\n",
" {'rcsb_id': '6LE6',\n",
" 'struct': {'title': 'Structure of LNLPTQGRAR bound FEM1C'}},\n",
" {'rcsb_id': '6LEY', 'struct': {'title': 'Structure of Sil1G bound FEM1C'}},\n",
" {'rcsb_id': '6LF0', 'struct': {'title': 'Structure of FEM1C'}},\n",
" {'rcsb_id': '6LKS',\n",
" 'struct': {'title': 'Effects of zinc ion on oligomerization and pH stability of influenza virus hemagglutinin'}},\n",
" {'rcsb_id': '6LM0',\n",
" 'struct': {'title': 'The crystal structure of cyanorhodopsin (CyR) N2098R from cyanobacteria Calothrix sp. NIES-2098'}},\n",
" {'rcsb_id': '6LM1',\n",
" 'struct': {'title': 'The crystal structure of cyanorhodopsin (CyR) N4075R from cyanobacteria Tolypothrix sp. NIES-4075'}},\n",
" {'rcsb_id': '6LPG', 'struct': {'title': 'human VASH1-SVBP complex'}},\n",
" {'rcsb_id': '6M2M',\n",
" 'struct': {'title': 'A role for histone chaperone OsChz1 in histone recognition and deposition'}},\n",
" {'rcsb_id': '6LTW',\n",
" 'struct': {'title': 'Crystal structure of Apo form of I122A/I330A variant of S-adenosylmethionine synthetase from Cryptosporidium hominis'}},\n",
" {'rcsb_id': '6LTV',\n",
" 'struct': {'title': 'Crystal Structure of I122A/I330A variant of S-adenosylmethionine synthetase from Cryptosporidium hominis in complex with ONB-SAM (2-nitro benzyme S-adenosyl-methionine)'}},\n",
" {'rcsb_id': '6LY5',\n",
" 'struct': {'title': 'Organization and energy transfer in a huge diatom PSI-FCPI supercomplex'}},\n",
" {'rcsb_id': '6S1A',\n",
" 'struct': {'title': 'Ligand binding domain of the P. putida receptor PcaY_PP'}},\n",
" {'rcsb_id': '6S18',\n",
" 'struct': {'title': 'Ligand binding domain of the P. putida receptor PcaY_PP in complex with glycerol'}},\n",
" {'rcsb_id': '6S33',\n",
" 'struct': {'title': 'Ligand binding domain of the P. putida receptor PcaY_PP in complex with Protocatechuate'}},\n",
" {'rcsb_id': '6S3B',\n",
" 'struct': {'title': 'Ligand binding domain of the P. putida receptor PcaY_PP in complex with benzoate'}},\n",
" {'rcsb_id': '6S37',\n",
" 'struct': {'title': 'Ligand binding domain of the P. putida receptor PcaY_PP in complex with salicylic acid'}},\n",
" {'rcsb_id': '6S38',\n",
" 'struct': {'title': 'Ligand binding domain of the P. putida receptor PcaY_PP in complex with quinate'}},\n",
" {'rcsb_id': '6S87',\n",
" 'struct': {'title': 'Crystal structure of 2-methylcitrate synthase (PrpC) from Pseudomonas aeruginosa in complex with oxaloacetate.'}},\n",
" {'rcsb_id': '6S96',\n",
" 'struct': {'title': 'Crystal structure of the catalytic domain of UBE2S C118A.'}},\n",
" {'rcsb_id': '6S98',\n",
" 'struct': {'title': 'Crystal structure of the catalytic domain of UBE2S WT.'}},\n",
" {'rcsb_id': '6T27',\n",
" 'struct': {'title': 'Structure of Human Aldose Reductase Mutant L301A with a Citrate Molecule Bound in the Anion Binding Pocket'}},\n",
" {'rcsb_id': '6T26',\n",
" 'struct': {'title': 'X-ray crystal structure of Vibrio alkaline phosphatase with the non-competitive inhibitor cyclohexylamine'}},\n",
" {'rcsb_id': '6TOQ',\n",
" 'struct': {'title': 'Crystal structure of a PP2A B56y/HTLV-1 integrase complex'}},\n",
" {'rcsb_id': '6TRS',\n",
" 'struct': {'title': 'Crystal structure of TFIIH subunit p52 in complex with p8'}},\n",
" {'rcsb_id': '6TRU',\n",
" 'struct': {'title': 'Crystal structure of the N-terminal half of the TFIIH subunit p52'}},\n",
" {'rcsb_id': '6TVS',\n",
" 'struct': {'title': \"Crystal structure of the haemagglutinin mutant (Gln226Leu) from an H10N7 seal influenza virus isolated in Germany in complex with avian receptor analogue 3'-SLN\"}},\n",
" {'rcsb_id': '6TVR',\n",
" 'struct': {'title': 'Crystal structure of the haemagglutinin mutant (Gln226Leu) from an H10N7 seal influenza virus isolated in Germany'}},\n",
" {'rcsb_id': '6TVT',\n",
" 'struct': {'title': \"Crystal structure of the haemagglutinin mutant (Gln226Leu, Del228) from an H10N7 seal influenza virus isolated in Germany in complex with human receptor analogue 6'-SLN\"}},\n",
" {'rcsb_id': '6TVA',\n",
" 'struct': {'title': \"Crystal structure of the haemagglutinin from a transmissible H10N7 seal influenza virus isolated in Netherland in complex with avian receptor analogue, 3'-SLN\"}},\n",
" {'rcsb_id': '6TVC',\n",
" 'struct': {'title': 'Crystal structure of the haemagglutinin from a transmissible H10N7 seal influenza virus isolated in Netherland'}},\n",
" {'rcsb_id': '6TVB',\n",
" 'struct': {'title': \"Crystal structure of the haemagglutinin from a transmissible H10N7 seal influenza virus isolated in Netherland in complex with human receptor analogue 6'-SLN\"}},\n",
" {'rcsb_id': '6TVD',\n",
" 'struct': {'title': \"Crystal structure of the haemagglutinin from a H10N7 seal influenza virus isolated in Germany in complex with avian receptor analogue, 3'-SLN\"}},\n",
" {'rcsb_id': '6TVF',\n",
" 'struct': {'title': \"Crystal structure of the haemagglutinin from a H10N7 seal influenza virus isolated in Germany in complex with human receptor analogue, 6'-SLN\"}},\n",
" {'rcsb_id': '6TWS',\n",
" 'struct': {'title': 'Crystal structure of the haemagglutinin mutant (Gln226Leu, Gly228Ser) from an H10N7 seal influenza virus isolated in Germany with 2mM EDTA'}},\n",
" {'rcsb_id': '6TWV',\n",
" 'struct': {'title': \"Crystal structure of the haemagglutinin mutant (Gln226Leu) from an H10N7 seal influenza virus isolated in Germany with human receptor analogue, 6'SLN\"}},\n",
" {'rcsb_id': '6TWI',\n",
" 'struct': {'title': \"Crystal structure of the haemagglutinin mutant (Gln226Leu, Gly228Ser) from an H10N7 seal influenza virus isolated in Germany in complex with avian receptor analogue 3'-SLN\"}},\n",
" {'rcsb_id': '6TWH',\n",
" 'struct': {'title': 'Crystal structure of the haemagglutinin mutant (Gln226Leu, Gly228Ser) from an H10N7 seal influenza virus isolated in Germany'}},\n",
" {'rcsb_id': '6TXO',\n",
" 'struct': {'title': \"Crystal structure of the haemagglutinin mutant (Gln226Leu, Del228) from an H10N7 seal influenza virus isolated in Germany in complex with avian receptor analogue 3'-SLN\"}},\n",
" {'rcsb_id': '6TY1',\n",
" 'struct': {'title': \"Crystal structure of the haemagglutinin mutant (Gln226Leu, Gly228Ser) from an H10N7 seal influenza virus isolated in Germany in complex with human receptor analogue 6'-SLN\"}},\n",
" {'rcsb_id': '6ULB',\n",
" 'struct': {'title': 'Sex Hormone-binding globulin mutant E176K in complex with Danazol'}},\n",
" {'rcsb_id': '6UOH',\n",
" 'struct': {'title': 'Asparaginase II from Escherichia coli'}},\n",
" {'rcsb_id': '6UP0',\n",
" 'struct': {'title': 'Structure of the Mango-III fluorescent aptamer bound to YO3-Biotin'}},\n",
" {'rcsb_id': '6UOD',\n",
" 'struct': {'title': 'Asparaginase II from Escherichia coli'}},\n",
" {'rcsb_id': '6UOG',\n",
" 'struct': {'title': 'Asparaginase II from Escherichia coli'}},\n",
" {'rcsb_id': '6UT4',\n",
" 'struct': {'title': 'Cryo-EM structure of the asymmetric AAA+ domain hexamer from Thermococcus gammatolerans McrB'}},\n",
" {'rcsb_id': '6UT3',\n",
" 'struct': {'title': 'X-ray structure of Thermococcus gammatolerans McrB AAA+ domain hexamer in P21 symmetry'}},\n",
" {'rcsb_id': '6V3V',\n",
" 'struct': {'title': 'Assembly of VIQKI I456(beta-L-homoisoleucine)with human parainfluenza virus type 3 (HPIV3) fusion glycoprotein N-terminal heptad repeat domain'}},\n",
" {'rcsb_id': '6UT6',\n",
" 'struct': {'title': 'Cryo-EM structure of the Escherichia coli McrBC complex'}},\n",
" {'rcsb_id': '6UT5',\n",
" 'struct': {'title': 'Cryo-EM structure of the Thermococcus gammatolerans McrBC complex'}},\n",
" {'rcsb_id': '6UT8',\n",
" 'struct': {'title': 'Refined half-complex from tetradecameric assembly of Thermococcus gammatolerans McrB AAA+ hexamers with bound McrC'}},\n",
" {'rcsb_id': '6UT7',\n",
" 'struct': {'title': 'Fitted model for the tetradecameric assembly of Thermococcus gammatolerans McrB AAA+ hexamers with bound McrC'}},\n",
" {'rcsb_id': '6OPP',\n",
" 'struct': {'title': 'Asymmetric model of CD4- and 17-bound B41 HIV-1 Env SOSIP in complex with DDM'}},\n",
" {'rcsb_id': '6OPO',\n",
" 'struct': {'title': 'Symmetric model of CD4- and 17-bound B41 HIV-1 Env SOSIP in complex with DDM'}},\n",
" {'rcsb_id': '6OPQ',\n",
" 'struct': {'title': 'CD4- and 17-bound HIV-1 Env B41 SOSIP frozen with LMNG'}},\n",
" {'rcsb_id': '6OPN',\n",
" 'struct': {'title': 'CD4- and 17-bound HIV-1 Env B41 SOSIP in complex with small molecule GO35'}},\n",
" {'rcsb_id': '6Y20',\n",
" 'struct': {'title': 'Crystal structure of Protein Scalloped (222-440) bound to Protein Vestigial (298-337)'}},\n",
" {'rcsb_id': '6XPP',\n",
" 'struct': {'title': 'Crystal structure of itaconate modified Mycobaterium tuberculosis isocitrate lyase'}},\n",
" {'rcsb_id': '6WQJ',\n",
" 'struct': {'title': 'Solution structure of vicilin-buried peptide-10 from cucumber'}},\n",
" {'rcsb_id': '6WQL',\n",
" 'struct': {'title': 'Solution structure of the seed peptide C2 (VBP-1) from pumpkin'}},\n",
" {'rcsb_id': '6X5C',\n",
" 'struct': {'title': 'Asymmetric model of CD4-bound B41 HIV-1 Env SOSIP in complex with small molecule GO52'}},\n",
" {'rcsb_id': '6X5B',\n",
" 'struct': {'title': 'Symmetric model of CD4- and 17-bound B41 HIV-1 Env SOSIP in complex with small molecule GO52'}},\n",
" {'rcsb_id': '6X8R',\n",
" 'struct': {'title': 'Pharmacological characterisation and NMR structure of the novel mu-conotoxin SxIIIC, a potent irreversible NaV channel inhibitor'}},\n",
" {'rcsb_id': '6Q2C',\n",
" 'struct': {'title': 'Domain-swapped dimer of Acanthamoeba castellanii CYP51'}},\n",
" {'rcsb_id': '6YHZ',\n",
" 'struct': {'title': 'UvrD helicase RNA polymerase interactions are governed by UvrDs carboxy terminal Tudor domain.'}},\n",
" {'rcsb_id': '6YI2',\n",
" 'struct': {'title': 'UvrD helicase RNA polymerase interactions are governed by UvrDs carboxy terminal Tudor domain.'}},\n",
" {'rcsb_id': '6YL4',\n",
" 'struct': {'title': 'Soluble epoxide hydrolase in complex with 3-((R)-3-(1-hydroxyureido)but-1-yn-1-yl)-N-((S)-3-phenyl-3-(4-trifluoromethoxy)phenyl)propyl)benzamide'}},\n",
" {'rcsb_id': '6Z1N',\n",
" 'struct': {'title': 'Structure of the human heterotetrameric cis-prenyltransferase complex'}},\n",
" {'rcsb_id': '6Z2Y',\n",
" 'struct': {'title': 'CryoEM structure of simian T-cell lymphotropic virus intasome in complex with PP2A regulatory subunit B56 gamma'}},\n",
" {'rcsb_id': '6Z7O',\n",
" 'struct': {'title': 'Crystal structure of Thioredoxin T from Drosophila melanogaster'}},\n",
" {'rcsb_id': '6Z8P',\n",
" 'struct': {'title': 'C-TERMINAL BROMODOMAIN OF HUMAN BRD2 WITH GSK973'}},\n",
" {'rcsb_id': '6Z7T',\n",
" 'struct': {'title': 'Nucleotide-free Myosin-II motor domain'}},\n",
" {'rcsb_id': '6Z7U',\n",
" 'struct': {'title': 'Myosin-II motor domain complexed with blebbistatin in a new ADP-release conformation'}},\n",
" {'rcsb_id': '6ZDM',\n",
" 'struct': {'title': \"Crystal structure of human heparanase in complex with a N',6O'-bis-sulfated 4-methylumbelliferyl heparan sulfate disaccharide\"}},\n",
" {'rcsb_id': '6ZFP',\n",
" 'struct': {'title': 'Cryo-EM structure of DNA-PKcs (State 2)'}},\n",
" {'rcsb_id': '6ZHA',\n",
" 'struct': {'title': 'Cryo-EM structure of DNA-PK monomer'}},\n",
" {'rcsb_id': '6ZH4',\n",
" 'struct': {'title': 'Cryo-EM structure of DNA-PKcs (State 3)'}},\n",
" {'rcsb_id': '6ZH6',\n",
" 'struct': {'title': 'Cryo-EM structure of DNA-PKcs:Ku80ct194'}},\n",
" {'rcsb_id': '6ZH8',\n",
" 'struct': {'title': 'Cryo-EM structure of DNA-PKcs:DNA'}},\n",
" {'rcsb_id': '6ZGL',\n",
" 'struct': {'title': 'Structure of DPS determined by movement-free cryoEM with zero dose extrapolation'}},\n",
" {'rcsb_id': '6ZH2',\n",
" 'struct': {'title': 'Cryo-EM structure of DNA-PKcs (State 1)'}},\n",
" {'rcsb_id': '6ZI7',\n",
" 'struct': {'title': 'Crystal structure of OleP-oleandolide(DEO) bound to L-rhamnose'}},\n",
" {'rcsb_id': '6ZHZ',\n",
" 'struct': {'title': 'OleP-oleandolide(DEO) in high salt crystallization conditions'}},\n",
" {'rcsb_id': '6ZI2',\n",
" 'struct': {'title': 'OleP-oleandolide(DEO) in low salt crystallization conditions'}},\n",
" {'rcsb_id': '6ZI3',\n",
" 'struct': {'title': 'Crystal structure of OleP-6DEB bound to L-rhamnose'}},\n",
" {'rcsb_id': '6ZHE',\n",
" 'struct': {'title': 'Cryo-EM structure of DNA-PK dimer'}},\n",
" {'rcsb_id': '7CMO',\n",
" 'struct': {'title': 'Crystal structure of human inorganic pyrophosphatase'}},\n",
" {'rcsb_id': '7CNG', 'struct': {'title': 'Structure of CDK5R1 bound FEM1B'}},\n",
" {'rcsb_id': '7D1A',\n",
" 'struct': {'title': 'cryo-EM structure of a group II intron RNP complexed with its reverse transcriptase'}},\n",
" {'rcsb_id': '7ANC',\n",
" 'struct': {'title': 'MlghC, GDP-mannoheptose C4 reductase from Campylobacter jejuni with NADP bound'}},\n",
" {'rcsb_id': '7AN4',\n",
" 'struct': {'title': 'MlghB, GDP-mannoheptose C3,5 epimerase from Campylobacter jejuni complex with GDP-mannose'}},\n",
" {'rcsb_id': '7CRP',\n",
" 'struct': {'title': 'NSD3 bearing E1181K/T1232A dual mutation in complex with 187-bp NCP (1:1 binding mode)'}},\n",
" {'rcsb_id': '7CRQ',\n",
" 'struct': {'title': 'NSD3 bearing E1181K/T1232A dual mutation in complex with 187-bp NCP (2:1 binding mode)'}},\n",
" {'rcsb_id': '7CRO',\n",
" 'struct': {'title': 'NSD2 bearing E1099K/T1150A dual mutation in complex with 187-bp NCP'}},\n",
" {'rcsb_id': '7CRR',\n",
" 'struct': {'title': 'Native NSD3 bound to 187-bp nucleosome'}},\n",
" {'rcsb_id': '7ANG',\n",
" 'struct': {'title': 'MlghB, GDP-mannoheptose C3,5 epimerase from Campylobacter jejuni'}},\n",
" {'rcsb_id': '7ANI',\n",
" 'struct': {'title': 'DdahB, GDP-mannoheptose C3,5 epimerase from Campylobacter jejuni'}},\n",
" {'rcsb_id': '7ANH', 'struct': {'title': 'DdhaC'}},\n",
" {'rcsb_id': '7ANJ',\n",
" 'struct': {'title': 'DdahB, GDP-mannoheptose C3,5 epimerase from Campylobacter jejuni complexed to GDP-mannose'}},\n",
" {'rcsb_id': '7D7R',\n",
" 'struct': {'title': 'Cryo-EM structure of the core domain of human ABCB6 transporter'}},\n",
" {'rcsb_id': '7D7N',\n",
" 'struct': {'title': 'Cryo-EM structure of human ABCB6 transporter'}},\n",
" {'rcsb_id': '7CZF',\n",
" 'struct': {'title': 'Crystal structure of Kaposi Sarcoma associated herpesvirus (KSHV ) gHgL in complex with the ligand binding domian (LBD) of EphA2'}},\n",
" {'rcsb_id': '7JGL',\n",
" 'struct': {'title': 'Crystal Structure of the Zn-bound Human Heavy-chain variant 122H-delta C-star with 2,5-furandihyrdoxamate collected at 100K'}},\n",
" {'rcsb_id': '7JGQ',\n",
" 'struct': {'title': 'Crystal Structure of the Ni-bound Human Heavy-chain variant 122H-delta C-star with 2,5-furandihyrdoxamate collected at 278K after one heating/cooling cycle'}},\n",
" {'rcsb_id': '7CZE',\n",
" 'struct': {'title': 'Crystal structure of Epstein-Barr virus (EBV) gHgL and in complex with the ligand binding domian (LBD) of EphA2'}},\n",
" {'rcsb_id': '6ZN3',\n",
" 'struct': {'title': 'Plasmodium facliparum glideosome trimeric sub-complex'}},\n",
" {'rcsb_id': '6ZMU',\n",
" 'struct': {'title': 'Crystal structure of the germline-specific thioredoxin protein Deadhead (Thioredoxin-1) from Drospohila melanogaster, P43212'}},\n",
" {'rcsb_id': '7JMS',\n",
" 'struct': {'title': 'Structure of the Hazara virus OTU bound to ubiquitin'}},\n",
" {'rcsb_id': '6ZPK',\n",
" 'struct': {'title': 'Crystal structure of the unconventional kinetochore protein Trypanosoma brucei KKT4 BRCT domain'}},\n",
" {'rcsb_id': '6ZPJ',\n",
" 'struct': {'title': 'Crystal structure of the unconventional kinetochore protein Leishmania mexicana KKT4 coiled coil domain'}},\n",
" {'rcsb_id': '6ZOV',\n",
" 'struct': {'title': 'ENTEROPEPTIDASE IN COMPLEX WITH COMPOUND 6'}},\n",
" {'rcsb_id': '6ZPM',\n",
" 'struct': {'title': 'Crystal structure of the unconventional kinetochore protein Trypanosoma cruzi KKT4 coiled coil domain'}},\n",
" {'rcsb_id': '6TJ5',\n",
" 'struct': {'title': 'T. gondii myosin A trimeric complex with ELC1'}},\n",
" {'rcsb_id': '6TJ4',\n",
" 'struct': {'title': 'P. falciparum essential light chain, N-terminal domain'}},\n",
" {'rcsb_id': '6TJ7',\n",
" 'struct': {'title': 'T. gondii myosin A trimeric complex'}},\n",
" {'rcsb_id': '6TJ6',\n",
" 'struct': {'title': 'T. gondii myosin A trimeric complex with ELC1, calcium-free'}},\n",
" {'rcsb_id': '6TJU',\n",
" 'struct': {'title': 'X-ray structure of C-terminal domain of human T-cell lymphotropic virus type 1 (HTLV-1)'}},\n",
" {'rcsb_id': '6TJW',\n",
" 'struct': {'title': 'Crystal structure of the haemagglutinin mutant (Gln226Leu, Del228) from an H10N7 seal influenza virus isolated in Germany'}},\n",
" {'rcsb_id': '6TJY',\n",
" 'struct': {'title': 'Crystal structure of haemagglutinin from (A/seal/Germany/1/2014) seal H10N7 influenza virus'}},\n",
" {'rcsb_id': '6TL0',\n",
" 'struct': {'title': 'Solution structure and 1H, 13C and 15N chemical shift assignments for the complex of VPS29 with VARP 687-747'}},\n",
" {'rcsb_id': '6TM2', 'struct': {'title': 'Human MUC2 AAs 21-1397'}}]}}"
]
},
"execution_count": 4,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"\n",
"#base graphql query:\n",
"url = 'https://data.rcsb.org/graphql'\n",
"\n",
"#this is an awkward way to write [\"code1\", \"code2\", \"code3\"]\n",
"v= '['\n",
"for i in pdb_codes[:-1]:\n",
" v+=\"\"\"\\\"\"\"\"+str(i)+\"\"\"\\\", \"\"\"\n",
"\n",
"v+=\"\"\"\\\"\"\"\"+str(pdb_codes[-1])+\"\"\"\\\"\"\"\" \n",
"v +=']'\n",
"v\n",
"\n",
"#put the query together\n",
"query = \"\"\"\n",
"{\n",
" entries(entry_ids:\"\"\" + v +\"\"\") {\n",
" rcsb_id\n",
" struct {\n",
" title\n",
" }\n",
" }\n",
"}\n",
"\"\"\"\n",
"\n",
"#encode as an html request and get the json data\n",
"r = requests.post(url, json={'query': query})\n",
"r.json()"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
}
],
"metadata": {
"kernelspec": {
"display_name": "Python 3",
"language": "python",
"name": "python3"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 3
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.7.8"
}
},
"nbformat": 4,
"nbformat_minor": 4
}
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