MolNFT v1 · #176679 · protein

Crystal structure of vim-2 mbl in complex with (R)-1-(sec-butyl)-1H- imidazole-2-carboxylic acid

7DUE · Beta-lactamase class B vim-2: “Crystal structure of vim-2 mbl in complex with (R)-1-(sec-butyl)-1H- imidazole-2-carboxylic acid”. X-ray diffraction, 2 ligands (HL3, ZN), 2 pockets (best druggability 0.73). MolNFT v1 #176679 on…

PDB: 7DUE
Type: protein
Length: 462 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: HL3, ZN
Pockets: 2 · best druggability 0.73

Structure

x-ray diffraction · 1 distinct chain · 27% helix, 30% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Beta-lactamase class B vim-2	protein	231	27% helix, 30% strand	Q9K2N0

Ligands and binding sites

HL3 · 1-[(2~{R})-butan-2-yl]imidazole-2-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	557	0.73	0.81	60	ZN, HL3
2	67	0.37	0.78	19	empty

Interfaces

1 interface between chains.

A–B · 592 Å² buried · 14 hydrogen bonds · protein-protein

Compared structures

7DUE · Crystal structure of VIM-2 MBL in complex with… · 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 7DUE · PDBe 7DUE · UniProt Q9K2N0

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