Research workbench
Pertussis toxin in complex with adpr and nicotinamide
Analyse Pertussis toxin in complex with adpr and nicotinamide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7SKK
- Type
- protein
- Length
- 720 residues
- Chains
- 4
- 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
- NCA, AR6, SO4
- Pockets
- 9 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 27% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Pertussis toxin subunit 1 (EC 2.4.2.-, 2.4.2.30) | protein | 180 | 26% helix, 28% strand | P04977 |
| C | Pertussis toxin subunit 1 (EC 2.4.2.-, 2.4.2.30) | protein | 179 | 30% helix, 28% strand | P04977 |
| D | Pertussis toxin subunit 1 (EC 2.4.2.-, 2.4.2.30) | protein | 181 | 26% helix, 30% strand | P04977 |
Ligands and binding sites
- NCA · Nicotinamide · ligand · 4 copies · chains A, B, C, D
- AR6 · [(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methyl [hydroxy-[[(2R,3S,4R,5S)-3,4,5-trihydroxyoxolan-2-yl]methoxy]phosphoryl] hydrogen phosphate · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 5 copies · chains B, C, A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 664 | 0.73 | 0.80 | 61 | empty |
| 2 | 597 | 0.71 | 0.79 | 57 | empty |
| 3 | 602 | 0.70 | 0.78 | 55 | empty |
| 4 | 309 | 0.63 | 0.80 | 32 | NCA, AR6 |
| 5 | 322 | 0.63 | 0.79 | 30 | NCA, AR6 |
Interfaces
4 interfaces between chains.
- A–B · 484 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 428 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 405 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 347 Ų buried · 5 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 7SKK · PDBe 7SKK · UniProt P04977
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