MolNFT v1 · #127905 · protein
Mono-zinc vim-5 metallo-beta-lactamase in complex with (1-chloro-4- hydroxyisoquinoline-3-carbonyl)-D-tryptophan (compound 1)
5NAI · Class B metallo-beta-lactamase: “Mono-zinc vim-5 metallo-beta-lactamase in complex with (1-chloro-4…”. X-ray diffraction, 3 ligands (93W, ZN, F), 1 pocket (best druggability 0.50). MolNFT v1 #127905 on GenesisL1: 3D structure…
- PDB
- 5NAI
- Type
- protein
- Length
- 231 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Class B metallo-beta-lactamase
- UniProt
- Q8GKX2
- Ligands
- 93W, ZN, F
- Pockets
- 1 · best druggability 0.50
Structure
x-ray diffraction · 1 distinct chain · 27% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Class B metallo-beta-lactamase | protein | 231 | 27% helix, 29% 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 · chains A
- ZN · Zinc ion · metal · 3 copies · chains A
- F · Fluoride ion · ion · 2 copies · chains A
- GOL · Glycerol · additive · chains A
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 | 179 | 0.50 | 0.77 | 26 | 93W |
Modifications
Observed in the structure: 1 modified (oxidation).
Compared structures
- 5NAI · 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 5NAI · PDBe 5NAI · UniProt Q8GKX2
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