Structure of PDB 1woi Chain D Binding Site BS01

Receptor Information

>1woi Chain D (length=303) Species: 1299 (Deinococcus radiodurans)

GPAHLPYGGIPTFARAPLVQPDGDWQADVAALGVPFDIALGFRPGARFAP
RALREASLRSVPPFTGLDGKTRLQGVTFADAGDVILPSLEPQLAHDRITE
AARQVRGRCRVPVFLGGDHSVSYPLLRAFADVPDLHVVQLDAHLDFTDTR
NDTKWSNSSPFRRACEALPNLVHITTVGLRGLRFDPEAVAAARARGHTII
PMDDVTADLAGVLAQLPRGQNVYFSVDVDGFDPAVIPGTSSPEPDGLTYA
QGMKILAAAAANNTVVGLDLVELAPNLDPTGRSELLMARLVMETLCEVFD
HVL

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: 1woi Chain D Residue 1507

Receptor-Ligand Complex Structure

Structure summary

• PDB: 1woi Crystal structure of agmatinase reveals structural conservation and inhibition mechanism of the ureohydrolase superfamily
• Resolution: 1.85 Å
• Binding residue (original residue number in PDB): H121 D143 D147 D229
• Binding residue (residue number reindexed from 1): H119 D141 D145 D227
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): H121 D143 H145 D147 N159 D229 D231 E274
• Catalytic site (residue number reindexed from 1): H119 D141 H143 D145 N157 D227 D229 E272
• Enzyme Commision number: 3.5.3.11: agmatinase.

Gene Ontology

Molecular Function

• 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:0033389 putrescine biosynthetic process from arginine, using agmatinase

External links

• PDB: RCSB:1woi, PDBe:1woi, PDBj:1woi
• PDBsum: 1woi
• PubMed: 15355972
• UniProt: Q9RZ04