Research workbench
Crystal structure of the metallo-beta-lactamase vim-2 with ML302F
Analyse Crystal structure of the metallo-beta-lactamase vim-2 with ML302F in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6EW3
- Type
- protein
- Length
- 462 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Metallo-beta-lactamase vim-2
- UniProt
- D1MEN9
- Ligands
- S3C, ZN, CL
- Pockets
- 1 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 27% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Metallo-beta-lactamase vim-2 | protein | 231 | 27% helix, 29% strand | D1MEN9 |
Ligands and binding sites
- S3C · (2Z)-2-sulfanyl-3-(2,3,6-trichlorophenyl)prop-2-enoic acid · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 6 copies · chains A, B
- CL · Chloride ion · ion · chains B
- FMT · Formic acid · additive · 4 copies · chains A, B
- DMS · Dimethyl sulfoxide · additive · 4 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 | 723 | 0.76 | 0.81 | 63 | ZN, S3C, DMS |
Interfaces
1 interface between chains.
- A–B · 608 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 6EW3 · Crystal structure of the metallo-beta-lactamase VIM-2 with ML302F · 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 D1MEN9
- Elsewhere: RCSB PDB 6EW3 · PDBe 6EW3 · UniProt D1MEN9
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