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Crystal structure of vim-2 complexed with compound 8

Analyse Crystal structure of vim-2 complexed with compound 8 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6DD0
Type: protein
Length: 460 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: P9T, ZN
Pockets: 3 · 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	230	27% helix, 30% strand	Q9K2N0

Ligands and binding sites

P9T · [(5,7-difluoro-2-oxo-2H-1-benzopyran-4-yl) methyl]phosphonic 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

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	545	0.73	0.81	53	ZN, P9T
2	95	0.41	0.78	21	empty
3	69	0.39	0.79	17	empty

Interfaces

1 interface between chains.

A–B · 612 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

6DD0 · Crystal structure of VIM-2 complexed with compound 8 · 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 6DD0 · PDBe 6DD0 · UniProt Q9K2N0

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