Research workbench
Di-zinc vim-5 metallo-beta-lactamase in complex with (1-chloro-4- hydroxyisoquinoline-3-carbonyl)-D-tryptophan (compound 1)
Analyse Di-zinc vim-5 metallo-beta-lactamase in complex with (1-chloro-4… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5N58
- Type
- protein
- Length
- 439 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Class B metallo-beta-lactamase
- UniProt
- Q8GKX2
- Ligands
- 93W, ZN
- Pockets
- 5 · best druggability 0.59
Structure
x-ray diffraction · 2 distinct chains · 26% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Class B metallo-beta-lactamase | protein | 220 | 25% helix, 30% strand | Q8GKX2 |
| B | Class B metallo-beta-lactamase | protein | 219 | 26% helix, 31% strand | Q8GKX2 |
Ligands and binding sites
- 93W · (2~{R})-2-[(1-chloranyl-4-oxidanyl-isoquinolin-3-yl) carbonylamino]-3-(1~{H}-indol-3-yl)propanoic acid · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 3 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 356 | 0.59 | 0.76 | 29 | empty |
| 2 | 182 | 0.56 | 0.80 | 26 | 93W, ZN |
| 3 | 150 | 0.56 | 0.81 | 22 | 93W |
| 4 | 133 | 0.44 | 0.76 | 28 | empty |
| 5 | 112 | 0.42 | 0.76 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 609 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5N58 · di-Zinc VIM-5 metallo-beta-lactamase in complex with… · 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 Q8GKX2
- Elsewhere: RCSB PDB 5N58 · PDBe 5N58 · UniProt Q8GKX2
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