Research workbench
The structure of the metallo-beta-lactamase vim-2 in complex with a triazolylthioacetamide inhibitor
Analyse The structure of the metallo-beta-lactamase vim-2 in complex with a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5LSC
- Type
- protein
- Length
- 470 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Metallo-beta-lactamase vim-2-like protein
- UniProt
- B8QIQ9
- Ligands
- 752, ZN, CL
- Pockets
- 2 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 26% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Metallo-beta-lactamase vim-2-like protein | protein | 235 | 26% helix, 29% strand | B8QIQ9 |
Ligands and binding sites
- 752 · 2-[5-[2-(1,3-benzothiazol-2-ylamino)-2-oxidanylidene-ethyl]sulfanyl-4~{H}-1,2,4-triazol-3-yl]benzoic acid · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 6 copies · chains A, B
- CL · Chloride ion · ion · 6 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.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 704 | 0.70 | 0.77 | 75 | CL, 752, ZN |
| 2 | 52 | 0.35 | 0.79 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 604 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 5LSC · The structure of the metallo-beta-lactamase VIM-2 in complex with 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 B8QIQ9
- Elsewhere: RCSB PDB 5LSC · PDBe 5LSC · UniProt B8QIQ9
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