Research workbench
The structure of imp-1 complexed with the detecting reagent (DANSYLC4SH) by a fluorescent probe
Analyse The structure of imp-1 complexed with the detecting reagent (DANSYLC4SH) by a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2DOO
- Type
- protein
- Length
- 432 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
- C4H, ZN
- Pockets
- 3 · best druggability 0.67
Structure
x-ray diffraction · 1 distinct chain · 27% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Beta-lactamase imp-1 (EC 3.5.2.6) | protein | 216 | 27% helix, 31% strand | P52699 |
Ligands and binding sites
- C4H · N-[4-({[5-(dimethylamino)-1-naphthyl]sulfonyl}amino)butyl]-3-sulfanylpropanamide · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 4 copies · chains A, B
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 | 540 | 0.67 | 0.78 | 48 | C4H |
| 2 | 400 | 0.63 | 0.78 | 40 | C4H |
| 3 | 73 | 0.34 | 0.76 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 391 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 2DOO · The structure of IMP-1 complexed with the detecting reagent (DansylC4SH) by a fluorescent… · 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 2DOO · PDBe 2DOO · UniProt P52699
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.