Research workbench
The crystal structure of pertussis toxin
Analyse The crystal structure of pertussis toxin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1PRT
- Type
- protein
- Length
- 1,868 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pertussis toxin (subunit S1); Pertussis toxin (subunit S2); Pertussis toxin (subunit S3)…
- UniProt
- P04977, P04978, P04979, P0A3R5, P04981
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 5 distinct chains · 21% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, G | Pertussis toxin (subunit S1) | protein | 224 | 33% helix, 27% strand | P04977 |
| B, H | Pertussis toxin (subunit S2) | protein | 196 | 15% helix, 36% strand | P04978 |
| C, I | Pertussis toxin (subunit S3) | protein | 196 | 20% helix, 37% strand | P04979 |
| D, E, J, K | Pertussis toxin (subunit S4) | protein | 110 | 14% helix, 55% strand | P0A3R5 |
| F, L | Pertussis toxin (subunit S5) | protein | 98 | 16% helix, 46% strand | P04981 |
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 657 | 0.77 | 0.82 | 81 | empty |
| 2 | 474 | 0.73 | 0.83 | 59 | empty |
| 3 | 52 | 0.72 | 0.99 | 18 | empty |
| 4 | 411 | 0.65 | 0.79 | 37 | empty |
| 5 | 63 | 0.65 | 0.93 | 22 | empty |
Interfaces
27 interfaces between chains.
- C–E · 1362 Ų buried · 22 hydrogen bonds · protein-protein
- I–K · 1352 Ų buried · 21 hydrogen bonds · protein-protein
- B–D · 1325 Ų buried · 22 hydrogen bonds · protein-protein
- H–J · 1322 Ų buried · 22 hydrogen bonds · protein-protein
- B–F · 1032 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 26 disulfide (disulfide).
Compared structures
- 1PRT · The crystal structure of pertussis toxin · the same entry in another collection · chain L against L, 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 1PRT · PDBe 1PRT · UniProt P04977 · UniProt P04978 · UniProt P04979 · UniProt P0A3R5 · UniProt P04981
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