MolNFT v1 · #4104 · protein
Imp-1 metallo beta-lactamase from pseudomonas aeruginosa in complex with a mercaptocarboxylate inhibitor
1DD6: “Imp-1 metallo beta-lactamase from pseudomonas aeruginosa in complex with a mercaptocarboxylate inhibitor”. X-ray diffraction, 3 ligands (MCI, ZN, SO4), 3 pockets (best druggability 0.52). MolNFT v1 #4104 on GenesisL1: 3D structure…
- PDB
- 1DD6
- Type
- protein
- Length
- 433 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Imp-1 metallo beta-lactamase
- EC
- 3.5.2.6
- UniProt
- P52699
- Ligands
- MCI, ZN, SO4
- Pockets
- 3 · best druggability 0.52
Structure
x-ray diffraction · 2 distinct chains · 27% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Imp-1 metallo beta-lactamase (EC 3.5.2.6) | protein | 216 | 27% helix, 32% strand | P52699 |
| B | Imp-1 metallo beta-lactamase (EC 3.5.2.6) | protein | 217 | 26% helix, 32% strand | P52699 |
Ligands and binding sites
- MCI · (2-mercaptomethyl-4-phenyl-butyrylimino)-(5-tetrazol-1-ylmethyl-thiophen-2-yl)-acetic acid · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 4 copies · chains A, B
- SO4 · Sulfate ion · ion · 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 220 | 0.52 | 0.77 | 28 | ZN, MCI |
| 2 | 193 | 0.50 | 0.76 | 31 | ZN, MCI |
| 3 | 62 | 0.38 | 0.79 | 14 | empty |
Compared structures
- 1DD6 · Imp-1 metallo beta-lactamase from pseudomonas aeruginosa in complex with a… · 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 1DD6 · PDBe 1DD6 · UniProt P52699
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