MolNFT v1 · #155189 · protein

Crystal structure of vim-2 metallo-beta-lactamase in complex with inhibitor X2

6KZN · Beta-lactamase class B vim-2: “Crystal structure of vim-2 metallo-beta-lactamase in complex with inhibitor X2”. X-ray diffraction, 2 ligands (E1C, ZN), 2 pockets (best druggability 0.72). MolNFT v1 #155189 on GenesisL1: 3D…

PDB: 6KZN
Type: protein
Length: 464 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Beta-lactamase class B vim-2
UniProt: Q9K2N0
Ligands: E1C, ZN
Pockets: 2 · best druggability 0.72

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Beta-lactamase class B vim-2	protein	232	27% helix, 29% strand	Q9K2N0

Ligands and binding sites

E1C · 2,5-diethyl-1-methyl-4-sulfamoyl-pyrrole-3-carboxylic acid · ligand · 2 copies · chains A, B
ZN · Zinc ion · metal · 6 copies · chains A, B
FMT · Formic acid · additive · 4 copies · chains A, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	551	0.72	0.80	55	E1C, ZN
2	68	0.38	0.79	23	empty

Interfaces

1 interface between chains.

A–B · 628 Å² buried · 14 hydrogen bonds · protein-protein

Compared structures

6KZN · Crystal Structure Of VIM-2 Metallo-beta-lactamase In Complex With Inhibitor X2 · 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 6KZN · PDBe 6KZN · UniProt Q9K2N0

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