MolNFT v1 · #176831 · protein

Crystal structure of vim-2 mbl in complex with 1-(but-3-en-1-yl)-4- methyl-1H-imidazole-2-carboxylic acid

7DYZ · Beta-lactamase class B vim-2: “Crystal structure of vim-2 mbl in complex with 1-(but-3-en-1-yl)-4- methyl-1H-imidazole-2-carboxylic acid”. X-ray diffraction, 2 ligands (HQR, ZN), 1 pocket (best druggability 0.55). MolNFT v1 #176831…

PDB: 7DYZ
Type: protein
Length: 231 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Beta-lactamase class B vim-2
UniProt: Q9K2N0
Ligands: HQR, ZN
Pockets: 1 · best druggability 0.55

Structure

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

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

Ligands and binding sites

HQR · 1-but-3-enyl-4-methyl-imidazole-2-carboxylic acid · ligand · chains A
ZN · Zinc ion · metal · 2 copies · chains A
GOL · Glycerol · additive · 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	177	0.55	0.80	22	ZN, HQR

Compared structures

7DYZ · 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 7DYZ · PDBe 7DYZ · UniProt Q9K2N0

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