Structure of PDB 3dj8 Chain A Binding Site BS02

Receptor Information
>3dj8 Chain A (length=313) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RTIGIIGAPFSKGQPRGGVEEGPTVLRKAGLLEKLKEQECDVKDYGDLPF
ADIPNDSPFQIVKNPRSVGKASEQLAGKVAEVKKNGRISLVLGGDHSLAI
GSISGHARVHPDLGVIWVDAHTDINTPLTTTSGNLHGQPVSFLLKELKGK
IPDVPGFSWVTPCISAKDIVYIGLRDVDPGEHYILKTLGIKYFSMTEVDR
LGIGKVMEETLSYLLGRKKRPIHLSFDVDGLDPSFTPATGTPVVGGLTYR
EGLYITEEIYKTGLLSGLDIMEVNPSLGKTPEEVTRTVNTAVAITLACFG
LAREGNHKPIDYL
Ligand information
Ligand IDMN
InChIInChI=1S/Mn/q+2
InChIKeyWAEMQWOKJMHJLA-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04
OpenEye OEToolkits 1.5.0		[Mn+2]
CACTVS 3.341[Mn++]
FormulaMn
NameMANGANESE (II) ION
ChEMBL
DrugBankDB06757
ZINC
PDB chain3dj8 Chain A Residue 515 [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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PDB3dj8 Synthesis of (2S)-2-amino-7,8-epoxyoctanoic acid and structure of its metal-bridging complex with human arginase I
Resolution1.51 Å
Binding residue
(original residue number in PDB)		H101 D124 D128 D232
Binding residue
(residue number reindexed from 1)		H96 D119 D123 D227
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) H101 D124 H126 D128 H141 D232 D234 E277
Catalytic site (residue number reindexed from 1) H96 D119 H121 D123 H136 D227 D229 E272
Enzyme Commision number 3.5.3.1: arginase.
Gene Ontology
Molecular Function
GO:0004053 arginase activity
GO:0005515 protein binding
GO:0016787 hydrolase activity
GO:0016813 hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amidines
GO:0030145 manganese ion binding
GO:0046872 metal ion binding
Biological Process
GO:0000050 urea cycle
GO:0002250 adaptive immune response
GO:0006525 arginine metabolic process
GO:0006527 arginine catabolic process
GO:0009624 response to nematode
GO:0019547 arginine catabolic process to ornithine
GO:0042130 negative regulation of T cell proliferation
GO:0042832 defense response to protozoan
GO:0045087 innate immune response
GO:0046007 negative regulation of activated T cell proliferation
GO:0060336 negative regulation of type II interferon-mediated signaling pathway
GO:0070965 positive regulation of neutrophil mediated killing of fungus
GO:2000552 negative regulation of T-helper 2 cell cytokine production
Cellular Component
GO:0005576 extracellular region
GO:0005615 extracellular space
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0035578 azurophil granule lumen
GO:0035580 specific granule lumen

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:3dj8, PDBe:3dj8, PDBj:3dj8
PDBsum3dj8
PubMed18802628
UniProtP05089|ARGI1_HUMAN Arginase-1 (Gene Name=ARG1)

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