Structure of PDB 3jbt Chain K Binding Site BS01

Receptor Information
>3jbt Chain K (length=1144) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GITSYVRTVLCEGGVPQRPVVFVTRKKLVNAIQQKLSKLKGEPGWVTIHG
MAGCGKSVLAAEAVRDHSLLEGCFPGGVHWVSVGKQDKSGLLMKLQNLCT
RLDQDESFSQRLPLNIEEAKDRLRILMLRKHPRSLLILDDVWDSWVLKAF
DSQCQILLTTRDKSVTDSVMGPKYVVPVESSLGKEKGLEILSLFVNMKKA
DLPEQAHSIIKECKGSPLVVSLIGALLRDFPNRWEYYLKQLQNKQFKRIR
KSSSYDYEALDEAMSISVEMLREDIKDYYTDLSILQKDVKVPTKVLCILW
DMETEEVEDILQEFVNKSLLFCDRNGKSFRYYLHDLQVDFLTEKNCSQLQ
DLHKKIITQFQRYHQPHTLSPDQEDCMYWYNFLAYHMASAKMHKELCALM
FSLDWIKAKTELVGPAHLIHEFVEYRHILDEKDCAVSENFQEFLSLNGHL
LGRQPFPNIVQLGLCEPETSEVYQQAKLQAKQEVDNGMLYLEWINKKNIT
NLSRLVVRPHTDAVYHACFSEDGQRIASCGADKTLQVFKAETGEKLLEIK
AHEDEVLCCAFSTDDRFIATCSVDKKVKIWNSMTGELVHTYDEHSEQVNC
CHFTNSSHHLLLATGSSDCFLKLWDLNQKECRNTMFGHTNSVNHCRFSPD
DKLLASCSADGTLKLWDATSANERKSINVKQFFLNLEDPQEDMEVIVKCC
SWSADGARIMVAAKNKIFLFDIHTSGLLGEIHTGHHSTIQYCDFSPQNHL
AVVALSQYCVELWNTDSRSKVADCRGHLSWVHGVMFSPDGSSFLTSSDDQ
TIRLWETKKVCKNSAVMLKQEVDVVFQENEVMVLAVDHIRRLQLINGRTG
QIDYLTEAQVSCCCLSPHLQYIAFGDENGAIEILELVNNRIFQSRFQHKK
TVWHIQFTADEKTLISSSDDAEIQVWNWQLDKCIFLRGHQETVKDFRLLK
NSRLLSWSFDGTVKVWNIITGNKEKDFVCHQGTVLSCDISHDATKFSSTS
ADKTAKIWSFDLLLPLHELRGHNGCVRCSAFSVDSTLLATGDDNGEIRIW
NVSNGELLHLCAPLSEEGAATHGGWVTDLCFSPDGKMLISAGGYIKWWNV
VTGESSQTFYTNGTNLKKIHVSPDFKTYVTVDNLGILYILQTLE
Ligand information
Ligand IDDTP
InChIInChI=1S/C10H16N5O12P3/c11-9-8-10(13-3-12-9)15(4-14-8)7-1-5(16)6(25-7)2-24-29(20,21)27-30(22,23)26-28(17,18)19/h3-7,16H,1-2H2,(H,20,21)(H,22,23)(H2,11,12,13)(H2,17,18,19)/t5-,6+,7+/m0/s1
InChIKeySUYVUBYJARFZHO-RRKCRQDMSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3C[C@@H]([C@H](O3)CO[P@](=O)(O)O[P@@](=O)(O)OP(=O)(O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3C[CH](O)[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O3
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3CC(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[C@H]3C[C@H](O)[C@@H](CO[P@@](O)(=O)O[P@](O)(=O)O[P](O)(O)=O)O3
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)CC3O
FormulaC10 H16 N5 O12 P3
Name2'-DEOXYADENOSINE 5'-TRIPHOSPHATE
ChEMBLCHEMBL335538
DrugBankDB03222
ZINCZINC000008215662
PDB chain3jbt Chain K Residue 1301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB3jbt Atomic structure of the apoptosome: mechanism of cytochrome c- and dATP-mediated activation of Apaf-1
Resolution3.8 Å
Binding residue
(original residue number in PDB)		V125 F126 V127 G159 K160 S161 V162 R265 S325 Y359
Binding residue
(residue number reindexed from 1)		V21 F22 V23 G55 K56 S57 V58 R161 S221 Y255
Annotation score4
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0008656 cysteine-type endopeptidase activator activity involved in apoptotic process
GO:0031072 heat shock protein binding
GO:0042802 identical protein binding
GO:0043531 ADP binding
Biological Process
GO:0001666 response to hypoxia
GO:0001822 kidney development
GO:0001843 neural tube closure
GO:0006915 apoptotic process
GO:0006919 activation of cysteine-type endopeptidase activity involved in apoptotic process
GO:0007399 nervous system development
GO:0007420 brain development
GO:0007584 response to nutrient
GO:0008635 activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c
GO:0010659 cardiac muscle cell apoptotic process
GO:0030154 cell differentiation
GO:0030900 forebrain development
GO:0042981 regulation of apoptotic process
GO:0043065 positive regulation of apoptotic process
GO:0051402 neuron apoptotic process
GO:0070059 intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress
GO:0071560 cellular response to transforming growth factor beta stimulus
GO:0072432 response to G1 DNA damage checkpoint signaling
GO:0097190 apoptotic signaling pathway
GO:0097193 intrinsic apoptotic signaling pathway
GO:1902510 regulation of apoptotic DNA fragmentation
GO:2001235 positive regulation of apoptotic signaling pathway
Cellular Component
GO:0005576 extracellular region
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0032991 protein-containing complex
GO:0034774 secretory granule lumen
GO:0043293 apoptosome
GO:0070062 extracellular exosome
GO:1904813 ficolin-1-rich granule lumen

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Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:3jbt, PDBe:3jbt, PDBj:3jbt
PDBsum3jbt
PubMed26543158
UniProtO14727|APAF_HUMAN Apoptotic protease-activating factor 1 (Gene Name=APAF1)

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