Research workbench
VIM-2 metallo-beta-lactamase in complex with ((S)-3-mercapto-2-methylpropanoyl)-L-tryptophan (Compound 4)
Analyse VIM-2 metallo-beta-lactamase in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5N4T
- Type
- protein
- Length
- 466 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.16
- Source
- Pseudomonas aeruginosa
- Molecule
- Beta-lactamase VIM-2
- UniProt
- Q9K2N0
- Ligands
- R59, BEZ, ZN
- Pockets
- 3 · best druggability 0.71
Structure
x-ray diffraction · resolution 1.16 · 2 distinct chains · 27% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-lactamase VIM-2 | protein | 234 | 26% helix, 29% strand | Q9K2N0 |
| B | Beta-lactamase VIM-2 | protein | 232 | 27% helix, 29% strand | Q9K2N0 |
Ligands and binding sites
- R59 · (2~{S})-3-(1~{H}-indol-3-yl)-2-[[(2~{S})-2-methyl-3-sulfanyl-propanoyl]amino]propanoic acid · ligand · 2 copies · chains A, B
- BEZ · Benzoic acid · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 6 copies · chains A, B
- FMT · Formic acid · additive · 3 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 619 | 0.71 | 0.79 | 58 | R59 |
| 2 | 72 | 0.42 | 0.80 | 19 | empty |
| 3 | 75 | 0.40 | 0.79 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 544 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 5N4T · Vim-2 metallo-beta-lactamase in complex with ((S)-3-mercapto-2… · 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 5N4T · PDBe 5N4T · UniProt Q9K2N0
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