Research workbench
Crystal structure of VIM-2 MBL in complex with (R)-1-(sec-butyl)-1H-imidazole-2-carboxylic acid
Analyse Crystal structure of VIM-2 MBL 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
- 7DUE
- Type
- protein
- Length
- 462 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.799
- Source
- Pseudomonas aeruginosa
- Molecule
- Beta-lactamase class B VIM-2
- UniProt
- Q9K2N0
- Ligands
- HL3, ZN
- Pockets
- 2 · best druggability 0.73
Structure
x-ray diffraction · resolution 1.799 · 1 distinct chain · 27% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Beta-lactamase class B VIM-2 | protein | 231 | 27% helix, 30% strand | Q9K2N0 |
Ligands and binding sites
- HL3 · 1-[(2~{R})-butan-2-yl]imidazole-2-carboxylic acid · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 6 copies · chains A, B
- FMT · Formic acid · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 557 | 0.73 | 0.81 | 60 | ZN, HL3 |
| 2 | 67 | 0.37 | 0.78 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 592 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 7DUE · Crystal structure of vim-2 mbl in complex with (R)-1-(sec-butyl)-1H… · 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 7DUE · PDBe 7DUE · UniProt Q9K2N0
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