MolNFT v1 · #187566 · protein
Pertussis toxin in complex with PJ34
7SKI · Pertussis toxin subunit 1: “Pertussis toxin in complex with PJ34”. X-ray diffraction, 1 ligand (P34), 4 pockets (best druggability 0.71). MolNFT v1 #187566 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7SKI
- Type
- protein
- Length
- 354 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pertussis toxin subunit 1
- EC
- 2.4.2.-, 2.4.2.30
- UniProt
- P04977
- Ligands
- P34
- Pockets
- 4 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pertussis toxin subunit 1 (EC 2.4.2.-, 2.4.2.30) | protein | 179 | 31% helix, 31% strand | P04977 |
| B | Pertussis toxin subunit 1 (EC 2.4.2.-, 2.4.2.30) | protein | 175 | 35% helix, 29% strand | P04977 |
Ligands and binding sites
- P34 · N~2~,N~2~-dimethyl-N~1~-(6-oxo-5,6-dihydrophenanthridin-2-yl)glycinamide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 535 | 0.71 | 0.80 | 48 | P34 |
| 2 | 207 | 0.63 | 0.83 | 30 | P34 |
| 3 | 92 | 0.37 | 0.75 | 15 | empty |
| 4 | 51 | 0.28 | 0.75 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1166 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
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 P04977
- Elsewhere: RCSB PDB 7SKI · PDBe 7SKI · UniProt P04977
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