Structure of PDB 3shf Chain A Binding Site BS02

Receptor Information

>3shf Chain A (length=1133) Species: 10090 (Mus musculus)

TDGGITSFVRTVLCEGGVPQRPVIFVTRKKLVHAIQQKLWKLNGEPGWVT
IYGMAGCGKSVLAAEAVRDHSLLEGCFSGGVHWVSIGKQDKSGLLMKLQN
LCMRLDQEESFSQRLPLNIEEAKDRLRVLMLRKHPRSLLILDDVWDPWVL
KAFDNQCQILLTTSDKSVTDSVMGPKHVVPVESGLGREKGLEILSLFVNM
KKEDLPAEAHSIIKECKGSPLVVSLIGALLRDFPNRWAYYLRQLQNKQFK
RIRKSSSYDYEALDEAMSISVEMLREDIKDYYTDLSILQKDVKVPTKVLC
VLWDLETEEVEDILQEFVNKSLLFCNRNGKSFCYYLHDLQVDFLTEKNRS
QLQDLHRKMVTQFQRYYQPHTLSPDQEDCMYWYNFLAYHMASANMHKELC
ALMFSLDWIKAKTELVGPAHLIHEFVAYRHILDEKDCAVCENFQEFLSLN
GHLLGRQPFPNIVQLGLCEPETSEVYRQAKLQAKQEGDTGRLYLEWINKK
TIKNLSRLVVRPHTDAVYHACFSQDGQRIASCGADKTLQVFKAETGEKLL
DIKAHEDEVLCCAFSSDDSYIATCSADKKVKIWDSATGKLVHTYDEHSEQ
VNCCHFTNKSNHLLLATGSNDFFLKLWDLNQKECRNTMFGHTNSVNHCRF
SPDDELLASCSADGTLRLWDVRSANERKSINVKRFFDVEVIVKCCSWSAD
GDKIIVAAKNKVLLFDIHTSGLLAEIHTGHHSTIQYCDFSPYDHLAVIAL
SQYCVELWNIDSRLKVADCRGHLSWVHGVMFSPDGSSFLTASDDQTIRVW
ETKKVCKNSAIVLKQEIDVVFQENETMVLAVDNIRGLQLIAGKTGQIDYL
PEAQVSCCCLSPHLEYVAFGDEDGAIKIIELPNNRVFSSGVGHKKAVRHI
QFTADGKTLISSSEDSVIQVWNWQTGDYVFLQAHQETVKDFRLLQDSRLL
SWSFDGTVKVWNVITGRIERDFTCHQGTVLSCAISSDATKFSSTSADKTA
KIWSFDLLSPLHELKGHNGCVRCSAFSLDGILLATGDDNGEIRIWNVSDG
QLLHSCAPISHGGWVTDVCFSPDSKTLVSAGGYLKWWNVATGDSSQTFYT
NGTNLKKIHVSPDFRTYVTVDNLGILYILQVLE

Ligand information

• Ligand ID: GBL
• InChI: InChI=1S/C4H6O2/c5-4-2-1-3-6-4/h1-3H2
• InChIKey: YEJRWHAVMIAJKC-UHFFFAOYSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: C1CC(=O)OC1
  ACDLabs 10.04: O=C1OCCC1
  CACTVS 3.341: O=C1CCCO1
• Formula: C4 H6 O2
• Name: GAMMA-BUTYROLACTONE;
  DIHYDROFURAN-2(3H)-ONE
• ChEMBL: CHEMBL95681
• DrugBank: DB04699
• ZINC: ZINC000004658567
• PDB chain: 3shf Chain A Residue 1251

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3shf Crystal structure of full-length Apaf-1: how the death signal is relayed in the mitochondrial pathway of apoptosis.
• Resolution: 3.55 Å
• Binding residue (original residue number in PDB): S387 L453 H457
• Binding residue (residue number reindexed from 1): S286 L352 H356
• Annotation score: 1

Gene Ontology

Molecular Function

• 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: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: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: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:0005634 nucleus
• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0032991 protein-containing complex
• GO:0043293 apoptosome

External links

• PDB: RCSB:3shf, PDBe:3shf, PDBj:3shf
• PDBsum: 3shf
• PubMed: 21827944
• UniProt: O88879|APAF_MOUSE Apoptotic protease-activating factor 1 (Gene Name=Apaf1)