Research workbench
Binary complex of pertussis toxin and ATP
Analyse Binary complex of pertussis toxin and ATP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1BCP
- Type
- protein
- Length
- 1,870 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pertussis toxin
- EC
- 2.4.2.-
- UniProt
- P04977, P04978, P04979, P0A3R5, P04981
- Ligands
- ATP
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 5 distinct chains · 22% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, G | Pertussis toxin (EC 2.4.2.-) | protein | 224 | 33% helix, 26% strand | P04977 |
| B, H | Pertussis toxin (EC 2.4.2.-) | protein | 197 | 20% helix, 33% strand | P04978 |
| C, I | Pertussis toxin (EC 2.4.2.-) | protein | 196 | 20% helix, 36% strand | P04979 |
| D, E, J, K | Pertussis toxin (EC 2.4.2.-) | protein | 110 | 14% helix, 55% strand | P0A3R5 |
| F, L | Pertussis toxin (EC 2.4.2.-) | protein | 98 | 14% helix, 39% strand | P04981 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, B, C, E, F, G, H, I, K, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 779 | 0.79 | 0.83 | 89 | ATP |
| 2 | 608 | 0.78 | 0.84 | 79 | ATP |
| 3 | 933 | 0.73 | 0.77 | 91 | empty |
| 4 | 56 | 0.73 | 0.99 | 21 | empty |
| 5 | 788 | 0.71 | 0.77 | 70 | empty |
Interfaces
27 interfaces between chains.
- I–K · 1384 Ų buried · 21 hydrogen bonds · protein-protein
- C–E · 1375 Ų buried · 20 hydrogen bonds · protein-protein
- H–J · 1325 Ų buried · 25 hydrogen bonds · protein-protein
- B–D · 1320 Ų buried · 25 hydrogen bonds · protein-protein
- H–L · 984 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 26 disulfide (disulfide).
Compared structures
- 1BCP · Binary complex of pertussis toxin and ATP · the same entry in another collection · chain K against K, TM-score 1.00
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
- Every structure of UniProt P04978
- Every structure of UniProt P04979
- Every structure of UniProt P0A3R5
- Every structure of UniProt P04981
- Elsewhere: RCSB PDB 1BCP · PDBe 1BCP · UniProt P04977 · UniProt P04978 · UniProt P04979 · UniProt P0A3R5 · UniProt P04981
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