MolNFT v1 · #25135 · protein
Structure-based design of the irreversible inhibitors to metallo--lactamase (imp-1)
1VGN · Beta-lactamase imp-1: “Structure-based design of the irreversible inhibitors to metallo--lactamase (imp-1)”. X-ray diffraction, 2 ligands (OPS, ZN), 3 pockets (best druggability 0.75). MolNFT v1 #25135 on GenesisL1: 3D structure…
- PDB
- 1VGN
- Type
- protein
- Length
- 435 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
- OPS, ZN
- Pockets
- 3 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 26% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-lactamase imp-1 (EC 3.5.2.6) | protein | 217 | 26% helix, 32% strand | P52699 |
| B | Beta-lactamase imp-1 (EC 3.5.2.6) | protein | 218 | 26% helix, 30% strand | P52699 |
Ligands and binding sites
- OPS · 3-oxo-3-[(3-oxopropyl)sulfanyl]propane-1-thiolate · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 4 copies · chains A, B
- ACY · Acetic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 363 | 0.75 | 0.86 | 52 | ZN, OPS |
| 2 | 414 | 0.69 | 0.80 | 51 | ZN, OPS |
| 3 | 81 | 0.35 | 0.75 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 671 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 1VGN · Structure-based design of the irreversible inhibitors to metallo--lactamase (IMP-1) · 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 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 1VGN · PDBe 1VGN · UniProt P52699
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