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The structure of a pertussis toxin-sugar complex as a model for receptor binding
Analyse The structure of a pertussis toxin-sugar complex as a model for receptor binding in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1PTO
- Type
- protein
- Length
- 1,870 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pertussis toxin (subunit S1); Pertussis toxin; Pertussis toxin (subunit S4); Pertussis…
- UniProt
- P04978, P04979, P04980, P04981
- Ligands
- GAL, SIA
- Pockets
- 20 · best druggability 0.75
Structure
x-ray diffraction · 6 distinct chains · 21% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, G | Pertussis toxin (subunit S1) | protein | 224 | 33% helix, 26% strand | — |
| B | Pertussis toxin | protein | 196 | 20% helix, 36% strand | P04978 |
| C, I | Pertussis toxin | protein | 196 | 19% helix, 37% strand | P04979 |
| D, E, J, K | Pertussis toxin (subunit S4) | protein | 110 | 13% helix, 48% strand | P04980 |
| F, L | Pertussis toxin (subunit S5) | protein | 98 | 15% helix, 46% strand | P04981 |
| H | Pertussis toxin (subunit S2) | protein | 198 | 19% helix, 35% strand | P04978 |
Ligands and binding sites
- GAL · beta-D-galactopyranose · sugar · 3 copies · chains C, I
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 3 copies · chains B, C, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 542 | 0.75 | 0.83 | 63 | empty |
| 2 | 551 | 0.75 | 0.82 | 64 | empty |
| 3 | 419 | 0.68 | 0.80 | 40 | empty |
| 4 | 61 | 0.67 | 0.95 | 20 | empty |
| 5 | 411 | 0.67 | 0.79 | 40 | empty |
Interfaces
27 interfaces between chains.
- I–K · 1382 Ų buried · 20 hydrogen bonds · protein-protein
- C–E · 1379 Ų buried · 21 hydrogen bonds · protein-protein
- H–J · 1353 Ų buried · 22 hydrogen bonds · protein-protein
- B–D · 1339 Ų buried · 22 hydrogen bonds · protein-protein
- B–F · 961 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 26 disulfide (disulfide).
Compared structures
- 1PTO · The structure of a pertussis toxin-sugar complex as a model for receptor binding · 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 P04978
- Every structure of UniProt P04979
- Every structure of UniProt P04980
- Every structure of UniProt P04981
- Elsewhere: RCSB PDB 1PTO · PDBe 1PTO · UniProt P04978 · UniProt P04979 · UniProt P04980 · UniProt P04981
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