Research workbench
Crystal structure of the di-zinc metallo-beta-lactamase vim- 4 from pseudomonas aeruginosa
Analyse Crystal structure of the di-zinc metallo-beta-lactamase vim- 4 from pseudomonas… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2WHG
- Type
- protein
- Length
- 460 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vim-4 metallo-beta-lactamase
- EC
- 3.5.2.6
- UniProt
- Q70E11
- Ligands
- ZN
- Pockets
- 4 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 27% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Vim-4 metallo-beta-lactamase (EC 3.5.2.6) | protein | 230 | 27% helix, 29% strand | Q70E11 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B
- FLC · Citrate anion · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 417 | 0.71 | 0.82 | 63 | ZN, FLC |
| 2 | 109 | 0.42 | 0.77 | 24 | empty |
| 3 | 56 | 0.37 | 0.80 | 20 | empty |
| 4 | 59 | 0.33 | 0.77 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 663 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 2WHG · Crystal Structure of the Di-Zinc Metallo-beta-lactamase VIM-4 from Pseudomonas aeruginosa · 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 Q70E11
- Elsewhere: RCSB PDB 2WHG · PDBe 2WHG · UniProt Q70E11
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