Structure of PDB 6jv4 Chain C Binding Site BS01

Receptor Information

>6jv4 Chain C (length=220) Species: 663 (Vibrio alginolyticus)

GTKELKLKKLSDNVYQHISYKRVEPWGLIGASGLVVINGTEAHMIDTPWT
TQGTKQLIEWIEAKGLTIKSAVVTHFHEDASGDIPLLNDLKIKTYATSLT
NKLLKLNQKEVSSDEISSNTFEFIDGVASVFYPGAGHTEDNIVVWLPNEK
ILFGGCFVKSLKNKNLGYTGDANISEWPNSMQKVINRYPDAKLVVPGHGE
VGDVSLLKHTQALALSAAAS

Ligand information

• Ligand ID: ZN
• InChI: InChI=1S/Zn/q+2
• InChIKey: PTFCDOFLOPIGGS-UHFFFAOYSA-N
• SMILES:
  CACTVS 3.341: [Zn++]
  ACDLabs 10.04
  OpenEye OEToolkits 1.5.0: [Zn+2]
• Formula: Zn
• Name: ZINC ION
• ChEMBL: CHEMBL1236970
• DrugBank: DB14532
• PDB chain: 6jv4 Chain C Residue 301

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6jv4 Genetic and Biochemical Characterization of VMB-1, a Novel Metallo-beta-Lactamase Encoded by a Conjugative, Broad-Host Range IncC Plasmid from Vibrio spp.
• Resolution: 1.7 Å
• Binding residue (original residue number in PDB): H78 H80 H140
• Binding residue (residue number reindexed from 1): H75 H77 H137
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): H78 H80 D82 H140 C159 K162 Y171 H201
• Catalytic site (residue number reindexed from 1): H75 H77 D79 H137 C156 K159 Y168 H198
• Enzyme Commision number: 3.5.2.6: beta-lactamase.

Gene Ontology

Molecular Function

• GO:0008270 zinc ion binding
• GO:0008800 beta-lactamase activity
• GO:0016787 hydrolase activity
• GO:0046872 metal ion binding

Biological Process

• GO:0017001 antibiotic catabolic process
• GO:0046677 response to antibiotic

Cellular Component

• GO:0042597 periplasmic space

External links

• PDB: RCSB:6jv4, PDBe:6jv4, PDBj:6jv4
• PDBsum: 6jv4
• PubMed: 32293144
• UniProt: A0A5Q5ADH9