MolNFT v1 · #166816 · protein

Structure of vim-2 bound to QPX7728 at 1.20 a

6V1P · Beta-lactamase class B vim-2: “Structure of vim-2 bound to QPX7728 at 1.20 a”. X-ray diffraction, 2 ligands (QNA, ZN), 2 pockets (best druggability 0.75). MolNFT v1 #166816 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 6V1P
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: QNA, ZN
Pockets: 2 · best druggability 0.75

Structure

x-ray diffraction · 2 distinct chains · 27% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Beta-lactamase class B vim-2	protein	230	27% helix, 30% strand	Q9K2N0
B	Beta-lactamase class B vim-2	protein	234	27% helix, 29% strand	Q9K2N0

Ligands and binding sites

QNA · (1~{A}~{R},7~{B}~{S})-5-fluoranyl-2,2-bis(oxidanyl)-1~{A},7~{B}-dihydro-1~{H}-cyclopropa[c][1, 2]benzoxaborinine-4-carboxylic acid · ligand · 2 copies · chains A, B
ZN · Zinc ion · metal · 6 copies · chains A, B
ACT · Acetate ion · additive · 4 copies · chains A, B
GOL · Glycerol · additive · 2 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	645	0.75	0.81	73	QNA, ZN, GOL
2	142	0.47	0.78	31	empty

Interfaces

1 interface between chains.

A–B · 573 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

6V1P · Structure of VIM-2 bound to QPX7728 at 1.20 A · 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 6V1P · PDBe 6V1P · UniProt Q9K2N0

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.