Research workbench
Crystal structure of metallo-beta-lactamase imp-1 mutant (D81E)
Analyse Crystal structure of metallo-beta-lactamase imp-1 mutant (D81E) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1WUP
- Type
- protein
- Length
- 867 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
- 9 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 28% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-lactamase imp-1 (EC 3.5.2.6) | protein | 217 | 27% helix, 27% strand | P52699 |
| B | Beta-lactamase imp-1 (EC 3.5.2.6) | protein | 216 | 28% helix, 28% strand | P52699 |
| C, D | Beta-lactamase imp-1 (EC 3.5.2.6) | protein | 217 | 28% helix, 27% strand | P52699 |
Ligands and binding sites
- ZN · Zinc ion · metal · 8 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
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 694 | 0.76 | 0.81 | 68 | ACY |
| 2 | 449 | 0.72 | 0.82 | 51 | ACY |
| 3 | 227 | 0.53 | 0.76 | 27 | empty |
| 4 | 173 | 0.48 | 0.77 | 24 | empty |
| 5 | 172 | 0.47 | 0.76 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–C · 890 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 812 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 664 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 1WUP · Crystal structure of metallo-beta-lactamase IMP-1 mutant (D81E) · 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 B 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 1WUP · PDBe 1WUP · UniProt P52699
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