MolNFT v1 · #26615 · protein
Crystal structure of metallo-beta-lactamase imp-1 mutant (D81A)
1WUO: “Crystal structure of metallo-beta-lactamase imp-1 mutant (D81A)”. X-ray diffraction, 1 ligand (ZN), 10 pockets (best druggability 0.75). MolNFT v1 #26615 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1WUO
- Type
- protein
- Length
- 876 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase imp-1
- EC
- 3.5.2.6
- UniProt
- P52699
- Ligands
- ZN
- Pockets
- 10 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 26% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Beta-lactamase imp-1 (EC 3.5.2.6) | protein | 219 | 26% helix, 30% strand | P52699 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- ACY · Acetic acid · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 784 | 0.75 | 0.79 | 84 | ACY |
| 2 | 185 | 0.51 | 0.78 | 25 | empty |
| 3 | 170 | 0.50 | 0.78 | 37 | ACY |
| 4 | 192 | 0.50 | 0.76 | 26 | empty |
| 5 | 50 | 0.41 | 0.83 | 17 | empty |
Interfaces
3 interfaces between chains.
- B–C · 824 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 605 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 562 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (oxidation).
Compared structures
- 1WUO · Crystal structure of metallo-beta-lactamase IMP-1 mutant (D81A) · the same entry in another collection · chain D against D, TM-score 1.00
- P52699 · AlphaFold monomer V2.0 prediction for metallo-beta-lactamase type 2 (P52699) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P52699
- Elsewhere: RCSB PDB 1WUO · PDBe 1WUO · UniProt P52699
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