Structure of PDB 6zyr Chain D Binding Site BS01

Receptor Information
>6zyr Chain D (length=219) Species: 615 (Serratia marcescens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SLPDLKIEKLDEGVYVHTSFEEVNGWGVVPKHGLVVLVNAEAYLIDTPFT
AKDTEKLVTWFVERGYKIKGSISSHFHSDSTGGIEWLNSRSIPTYASELT
NELLKKDGKVQATNSFSGVNYWLVKNKIEVFYPGPGHTPDNVVVWLPERK
ILFGGCFIKPYGLGNLGDANIEAWPKSAKLLKSKYGKAKLVVPSHSEVGD
ASLLKLTLEQAVKGLNESK
Ligand information
Ligand IDZN
InChIInChI=1S/Zn/q+2
InChIKeyPTFCDOFLOPIGGS-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.341[Zn++]
ACDLabs 10.04
OpenEye OEToolkits 1.5.0		[Zn+2]
FormulaZn
NameZINC ION
ChEMBLCHEMBL1236970
DrugBankDB14532
ZINC
PDB chain6zyr Chain D Residue 301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB6zyr 2-Mercaptomethyl-thiazolidines use conserved aromatic-S interactions to achieve broad-range inhibition of metallo-beta-lactamases.
Resolution1.87 Å
Binding residue
(original residue number in PDB)		D81 C158 H197
Binding residue
(residue number reindexed from 1)		D79 C156 H195
Annotation score1
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6zyr, PDBe:6zyr, PDBj:6zyr
PDBsum6zyr
PubMed34164056
UniProtP52699|BLAB_SERMA Metallo-beta-lactamase type 2

[Back to BioLiP]