MolNFT v1 · #187621 · protein
Pertussis toxin S1 subunit bound to baad
7SNE · Pertussis toxin subunit 1: “Pertussis toxin S1 subunit bound to baad”. X-ray diffraction, 1 ligand (9XR), 7 pockets (best druggability 0.75). MolNFT v1 #187621 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7SNE
- Type
- protein
- Length
- 722 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
- 9XR
- Pockets
- 7 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 28% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pertussis toxin subunit 1 (EC 2.4.2.-, 2.4.2.30) | protein | 180 | 26% helix, 28% strand | P04977 |
| B, D | Pertussis toxin subunit 1 (EC 2.4.2.-, 2.4.2.30) | protein | 181 | 30% helix, 28% strand | P04977 |
| C | Pertussis toxin subunit 1 (EC 2.4.2.-, 2.4.2.30) | protein | 180 | 28% helix, 28% strand | P04977 |
Ligands and binding sites
- 9XR · [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl [(2R,3S,4R,5S)-5-(3-carbamoylanilino)-3,4-dihydroxyoxolan-2-yl]methyl dihydrogen diphosphate (non-preferred name) · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 533 | 0.75 | 0.83 | 62 | empty |
| 2 | 710 | 0.75 | 0.81 | 67 | empty |
| 3 | 801 | 0.74 | 0.79 | 77 | empty |
| 4 | 414 | 0.64 | 0.78 | 43 | 9XR |
| 5 | 295 | 0.60 | 0.78 | 32 | 9XR |
Interfaces
4 interfaces between chains.
- B–D · 556 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 466 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 450 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 435 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 7SNE · PDBe 7SNE · UniProt P04977
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