MolNFT v1 · #87440 · protein
Crystal structure of the metallo-beta-lactamase imp-1 with L-captopril
4C1F: “Crystal structure of the metallo-beta-lactamase imp-1 with L-captopril”. X-ray diffraction, 3 ligands (X8Z, ZN, SO4), 2 pockets (best druggability 0.78). MolNFT v1 #87440 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4C1F
- Type
- protein
- Length
- 436 residues
- Chains
- 2
- 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
- X8Z, ZN, SO4
- Pockets
- 2 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 28% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-lactamase imp-1 (EC 3.5.2.6) | protein | 219 | 28% helix, 32% strand | P52699 |
| B | Beta-lactamase imp-1 (EC 3.5.2.6) | protein | 217 | 27% helix, 30% strand | P52699 |
Ligands and binding sites
- X8Z · L-captopril · ligand · chains A, B
- ZN · Zinc ion · metal · 4 copies · chains A, B
- SO4 · Sulfate ion · ion · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 701 | 0.78 | 0.82 | 75 | X8Z |
| 2 | 331 | 0.66 | 0.81 | 39 | ZN |
Interfaces
1 interface between chains.
- A–B · 750 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 4C1F · Crystal structure of the metallo-beta-lactamase IMP-1 with L-captopril · the same entry in another collection · chain A against A, 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 4C1F · PDBe 4C1F · UniProt P52699
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