Structure of PDB 6zyr Chain B Binding Site BS01

Receptor Information

>6zyr Chain B (length=219) Species: 615 (Serratia marcescens)

SLPDLKIEKLDEGVYVHTSFEEVNGWGVVPKHGLVVLVNAEAYLIDTPFT
AKDTEKLVTWFVERGYKIKGSISSHFHSDSTGGIEWLNSRSIPTYASELT
NELLKKDGKVQATNSFSGVNYWLVKNKIEVFYPGPGHTPDNVVVWLPERK
ILFGGCFIKPYGLGNLGDANIEAWPKSAKLLKSKYGKAKLVVPSHSEVGD
ASLLKLTLEQAVKGLNESK

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: 6zyr Chain B Residue 301

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6zyr 2-Mercaptomethyl-thiazolidines use conserved aromatic-S interactions to achieve broad-range inhibition of metallo-beta-lactamases.
• Resolution: 1.87 Å
• Binding residue (original residue number in PDB): H77 H79 H139
• Binding residue (residue number reindexed from 1): H75 H77 H137
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): H77 H79 D81 H139 C158 K161 N167 H197
• Catalytic site (residue number reindexed from 1): H75 H77 D79 H137 C156 K159 N165 H195
• 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:6zyr, PDBe:6zyr, PDBj:6zyr
• PDBsum: 6zyr
• PubMed: 34164056
• UniProt: P52699|BLAB_SERMA Metallo-beta-lactamase type 2