MolNFT v1 · #172549 · protein

Structure of vim-2 metallo-beta-lactamase with hydrolysed faropenem imine product

7A5Z · Beta-lactamase vim-2: “Structure of vim-2 metallo-beta-lactamase with hydrolysed faropenem imine product”. X-ray diffraction, 5 ligands (QZH, ZN, MG), 1 pocket (best druggability 0.58). MolNFT v1 #172549 on GenesisL1: 3D structure…

PDB: 7A5Z
Type: protein
Length: 231 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Beta-lactamase vim-2
UniProt: Q9K2N0
Ligands: QZH, ZN, MG, NA, CL
Pockets: 1 · best druggability 0.58

Structure

x-ray diffraction · 1 distinct chain · 27% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Beta-lactamase vim-2	protein	231	27% helix, 29% strand	Q9K2N0

Ligands and binding sites

QZH · (5~{Z})-2-[1,3-bis(oxidanyl)-1-oxidanylidene-butan-2-yl]-5-(4-oxidanylbutylidene)-2~{H}-1,3-thiazole-4-carboxylic acid · ligand · chains A
ZN · Zinc ion · metal · 3 copies · chains A
MG · Magnesium ion · metal · chains A
NA · Sodium ion · metal · chains A
CL · Chloride ion · ion · 2 copies · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	169	0.58	0.82	25	QZH, ZN, NA

Compared structures

7A5Z · Structure of VIM-2 metallo-beta-lactamase with hydrolysed Faropenem imine product · the same entry in another collection · chain A against A, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt Q9K2N0
Elsewhere: RCSB PDB 7A5Z · PDBe 7A5Z · UniProt Q9K2N0

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