Structure of PDB 6vst Chain B Binding Site BS01

Receptor Information

>6vst Chain B (length=318) Species: 3880 (Medicago truncatula)

SPALLEKAQNRVIDAALTFIRERAKFKGELMRSLGGVAATSSLLGVPLGH
HSSFHEGSAFAPPRIREAIWCDSTNSTTEEGKNLRDPRVITNVGDVPIEE
IRDCGVDDKRLANVISESVKLVMDEDPLRPLVLGGDHSISFPVVRAVSEK
LGGAVDILHFDAHPDLYHDFEGNYYSHASPFARIMEGGYARRLVQVGIRS
ITNDVREQVKKYGVETHEMRTLSRDRPILENLKLGEGVKGVYVSIDVDSL
DPSIAPGVSHHEPGGLLFRDILNILQNLQGDIVGGDVVEYNPQRDTYDGI
TALVAAKLVRELAAKMSK

Ligand information

• Ligand ID: MN
• InChI: InChI=1S/Mn/q+2
• InChIKey: WAEMQWOKJMHJLA-UHFFFAOYSA-N
• SMILES:
  ACDLabs 10.04
  OpenEye OEToolkits 1.5.0: [Mn+2]
  CACTVS 3.341: [Mn++]
• Formula: Mn
• Name: MANGANESE (II) ION
• DrugBank: DB06757
• PDB chain: 6vst Chain B Residue 401

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6vst The Neighboring Subunit Is Engaged to Stabilize the Substrate in the Active Site of Plant Arginases.
• Resolution: 2.12 Å
• Binding residue (original residue number in PDB): D181 H183 D266 D268
• Binding residue (residue number reindexed from 1): D161 H163 D246 D248
• Annotation score: 1

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

External links

• PDB: RCSB:6vst, PDBe:6vst, PDBj:6vst
• PDBsum: 6vst
• PubMed: 32754173
• UniProt: G7JFU5|ARGI_MEDTR Arginase, mitochondrial (Gene Name=ARGAH)