Structure of PDB 5nfo Chain B Binding Site BS02

Receptor Information
>5nfo Chain B (length=318) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SHMAEAALEAVRSELREFPAAARELCVPLAVPYLDKPPTPLHFYRDWVCP
NRPCIIRNALQHWPALQKWSLPYFRATVGSTEVSVAVTPDGYADAVRGDR
FMMPAERRLPLSFVLDVLEGRAQHPGVLYVQKQCSNLPSELPQLLPDLES
HVPWASEALGKMPDAVNFWLGEAAAVTSLHKDHYENLYCVVSGEKHFLFH
PPSDRPFIPYELYTPATYQLTEEGTFKVVDEEAMEKVPWIPLDPLAPDLA
RYPSYSQAQALCCTVRAGEMLYLPALWFHHVQQSQGCIAVNFWYDMEYDL
KYSYFQLLDSLTKASGLD
Ligand information
Ligand IDAKG
InChIInChI=1S/C5H6O5/c6-3(5(9)10)1-2-4(7)8/h1-2H2,(H,7,8)(H,9,10)
InChIKeyKPGXRSRHYNQIFN-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=C(O)C(=O)CCC(=O)O
OpenEye OEToolkits 1.7.6C(CC(=O)O)C(=O)C(=O)O
CACTVS 3.385OC(=O)CCC(=O)C(O)=O
FormulaC5 H6 O5
Name2-OXOGLUTARIC ACID
ChEMBLCHEMBL1686
DrugBankDB08845
ZINCZINC000001532519
PDB chain5nfo Chain B Residue 502 [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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PDB5nfo (3S)-Lysyl hydroxylation of TRAFAC GTPases is catalyzed by the human Jumonji-C oxygenase JMJD7.
Resolution2.173 Å
Binding residue
(original residue number in PDB)		Y127 W167 T175 H178 N184 Y186 H277 V279 W291
Binding residue
(residue number reindexed from 1)		Y129 W169 T177 H180 N186 Y188 H279 V281 W293
Annotation score5
Enzymatic activity
Enzyme Commision number 1.14.11.63: peptidyl-lysine (3S)-dioxygenase.
3.4.-.-
Gene Ontology
Molecular Function
GO:0004175 endopeptidase activity
GO:0004177 aminopeptidase activity
GO:0004497 monooxygenase activity
GO:0005515 protein binding
GO:0016706 2-oxoglutarate-dependent dioxygenase activity
GO:0035064 methylated histone binding
GO:0046872 metal ion binding
GO:0106155 peptidyl-lysine 3-dioxygenase activity
Biological Process
GO:0006508 proteolysis
GO:0018126 protein hydroxylation
Cellular Component
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005829 cytosol

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5nfo, PDBe:5nfo, PDBj:5nfo
PDBsum5nfo
PubMed
UniProtP0C870|JMJD7_HUMAN Bifunctional peptidase and (3S)-lysyl hydroxylase JMJD7 (Gene Name=JMJD7)

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