Research workbench
Crystal structure of the metallo-beta-lactamase vim-2 with D-captopril
Analyse Crystal structure of the metallo-beta-lactamase vim-2 with D-captopril in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4C1E
- Type
- protein
- Length
- 462 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase class B vim-2
- EC
- 3.5.2.6
- UniProt
- Q9K2N0
- Ligands
- MCO, ZN, NA
- Pockets
- 1 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 27% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Beta-lactamase class B vim-2 (EC 3.5.2.6) | protein | 231 | 27% helix, 29% strand | Q9K2N0 |
Ligands and binding sites
- MCO · 1-(3-mercapto-2-methyl-propionyl)-pyrrolidine-2-carboxylic acid · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 6 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
- FMT · Formic acid · additive · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 484 | 0.69 | 0.80 | 49 | MCO, ZN |
Interfaces
1 interface between chains.
- A–B · 537 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 4C1E · Crystal structure of the metallo-beta-lactamase VIM-2 with D-captopril · 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 4C1E · PDBe 4C1E · UniProt Q9K2N0
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.