MolNFT v1 · #158825 · protein

Crystal structure of vim-2 with compound 16

6O5T · Beta-lactamase class B vim-2: “Crystal structure of vim-2 with compound 16”. X-ray diffraction, 2 ligands (L8J, ZN), 3 pockets (best druggability 0.71). MolNFT v1 #158825 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6O5T
Type: protein
Length: 466 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: L8J, ZN
Pockets: 3 · best druggability 0.71

Structure

x-ray diffraction · 1 distinct chain · 26% helix, 30% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Beta-lactamase class B vim-2	protein	233	26% helix, 30% strand	Q9K2N0

Ligands and binding sites

L8J · [(5,7-dibromo-2-oxo-1,2-dihydroquinolin-4-yl) methyl]phosphonic acid · ligand · 2 copies · chains A, B
ZN · Zinc ion · metal · 8 copies · chains A, B
ACT · Acetate ion · additive · 7 copies · chains A, B

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

Pockets

3 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	553	0.71	0.80	54	L8J
2	108	0.47	0.80	28	empty
3	51	0.31	0.77	19	empty

Interfaces

1 interface between chains.

A–B · 543 Å² buried · 12 hydrogen bonds · protein-protein

Compared structures

6O5T · Crystal Structure of VIM-2 with Compound 16 · 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 6O5T · PDBe 6O5T · UniProt Q9K2N0

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