Research workbench
Mono-zinc vim-5 metallo-beta-lactamase in complex with (1-chloro-4- hydroxyisoquinoline-3-carbonyl)-L-tryptophan (compound 2)
Analyse Mono-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
- 5N55
- Type
- protein
- Length
- 689 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Class B metallo-beta-lactamase
- UniProt
- Q8GKX2
- Ligands
- 8NN, ZN
- Pockets
- 3 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 27% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Class B metallo-beta-lactamase | protein | 230 | 28% helix, 28% strand | Q8GKX2 |
| B | Class B metallo-beta-lactamase | protein | 231 | 27% helix, 29% strand | Q8GKX2 |
| C | Class B metallo-beta-lactamase | protein | 228 | 27% helix, 29% strand | Q8GKX2 |
Ligands and binding sites
- 8NN · (1-chloro-4-hydroxyisoquinoline-3-carbonyl)-L-tryptophan · ligand · 3 copies · chains A, B, C
- ZN · Zinc ion · metal · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 663 | 0.78 | 0.83 | 95 | 8NN |
| 2 | 144 | 0.52 | 0.80 | 28 | 8NN |
| 3 | 263 | 0.47 | 0.73 | 39 | empty |
Interfaces
2 interfaces between chains.
- A–B · 706 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 125 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 modified (nonstandard).
Compared structures
- 5N55 · mono-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 5N55 · PDBe 5N55 · UniProt Q8GKX2
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