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Structure of the vim-2 metallo-beta-lactamase in complex with a bisthiazolidine inhibitor
Analyse Structure of the vim-2 metallo-beta-lactamase in complex with a bisthiazolidine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4UA4
- 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
- 3C7, ZN
- Pockets
- 3 · best druggability 0.67
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 | 26% helix, 30% strand | Q9K2N0 |
| B | Beta-lactamase class B vim-2 | protein | 234 | 28% helix, 28% strand | Q9K2N0 |
Ligands and binding sites
- 3C7 · (3R,5R,7aS)-5-(sulfanylmethyl)tetrahydro[1,3]thiazolo[4,3-b][1,3]thiazole-3-carboxylic acid · ligand · 3 copies · chains A, B
- ZN · Zinc ion · metal · 4 copies · chains A, B
- GOL · Glycerol · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 279 | 0.67 | 0.83 | 33 | 3C7 |
| 2 | 138 | 0.53 | 0.81 | 26 | GOL |
| 3 | 167 | 0.53 | 0.79 | 20 | 3C7 |
Interfaces
1 interface between chains.
- A–B · 478 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 4UA4 · Structure of the VIM-2 Metallo-beta-Lactamase in Complex with a Bisthiazolidine Inhibitor · 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 4UA4 · PDBe 4UA4 · UniProt Q9K2N0
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