MolNFT v1 · #113125 · protein
Approved drugs containing thiols as inhibitors of metallo-beta- lactamases: strategy to combat multidrug-resistant bacteria
5A5Z · Beta-lactamase ndm-1: “Approved drugs containing thiols as inhibitors of metallo-beta- lactamases: strategy to combat…”. X-ray diffraction, 2 ligands (WJZ, ZN), 3 pockets (best druggability 0.78). MolNFT v1 #113125 on GenesisL1: 3D…
- PDB
- 5A5Z
- Type
- protein
- Length
- 472 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase ndm-1
- EC
- 3.5.2.6
- UniProt
- C7C422
- Ligands
- WJZ, ZN
- Pockets
- 3 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 23% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Beta-lactamase ndm-1 (EC 3.5.2.6) | protein | 236 | 23% helix, 31% strand | C7C422 |
Ligands and binding sites
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 | 101 | 0.78 | 0.98 | 20 | empty |
| 2 | 147 | 0.43 | 0.75 | 25 | ZN, WJZ |
| 3 | 106 | 0.37 | 0.74 | 20 | ZN, WJZ |
Interfaces
1 interface between chains.
- A–C · 906 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5A5Z · Approved Drugs Containing Thiols as Inhibitors of Metallo-beta- lactamases: Strategy To… · the same entry in another collection · chain A against A, TM-score 1.00
- C7C422 · AlphaFold monomer V2.0 prediction for metallo-beta-lactamase type 2 (C7C422) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 C7C422
- Elsewhere: RCSB PDB 5A5Z · PDBe 5A5Z · UniProt C7C422
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