Structure of PDB 6vst Chain L Binding Site BS03

Receptor Information
>6vst Chain L (length=319) Species: 3880 (Medicago truncatula) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VSPALLEKAQNRVIDAALTFIRERAKFKGELMRSLGGVAATSSLLGVPLG
HHSSFHEGSAFAPPRIREAIWCDSTNSTTEEGKNLRDPRVITNVGDVPIE
EIRDCGVDDKRLANVISESVKLVMDEDPLRPLVLGGDHSISFPVVRAVSE
KLGGAVDILHFDAHPDLYHDFEGNYYSHASPFARIMEGGYARRLVQVGIR
SITNDVREQVKKYGVETHEMRTLSRDRPILENLKLGEGVKGVYVSIDVDS
LDPSIAPGVSHHEPGGLLFRDILNILQNLQGDIVGGDVVEYNPQRDTYDG
ITALVAAKLVRELAAKMSK
Ligand information
Ligand IDORN
InChIInChI=1S/C5H12N2O2/c6-3-1-2-4(7)5(8)9/h4H,1-3,6-7H2,(H,8,9)/t4-/m0/s1
InChIKeyAHLPHDHHMVZTML-BYPYZUCNSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6C(C[C@@H](C(=O)O)N)CN
CACTVS 3.370NCCC[CH](N)C(O)=O
CACTVS 3.370NCCC[C@H](N)C(O)=O
ACDLabs 12.01O=C(O)C(N)CCCN
OpenEye OEToolkits 1.7.6C(CC(C(=O)O)N)CN
FormulaC5 H12 N2 O2
NameL-ornithine
ChEMBLCHEMBL446143
DrugBankDB00129
ZINCZINC000001532530
PDB chain6vst Chain L Residue 403 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6vst The Neighboring Subunit Is Engaged to Stabilize the Substrate in the Active Site of Plant Arginases.
Resolution2.12 Å
Binding residue
(original residue number in PDB)		H183 Y187 H197 H280
Binding residue
(residue number reindexed from 1)		H164 Y168 H178 H261
Annotation score5
Enzymatic activity
Enzyme Commision number 3.5.3.1: arginase.
3.5.3.11: agmatinase.
Gene Ontology
Molecular Function
GO:0004053 arginase activity
GO:0008783 agmatinase activity
GO:0016787 hydrolase activity
GO:0016813 hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amidines
GO:0046872 metal ion binding
Biological Process
GO:0000050 urea cycle
GO:0006525 arginine metabolic process
GO:0009446 putrescine biosynthetic process
GO:0019547 arginine catabolic process to ornithine
GO:0033388 putrescine biosynthetic process from arginine
GO:0033389 putrescine biosynthetic process from arginine, using agmatinase
GO:0034214 protein hexamerization
Cellular Component
GO:0005739 mitochondrion

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:6vst, PDBe:6vst, PDBj:6vst
PDBsum6vst
PubMed32754173
UniProtG7JFU5|ARGI_MEDTR Arginase, mitochondrial (Gene Name=ARGAH)

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