MolNFT v1 · #97195 · protein
Structure of typhoid toxin
4K6L · Putative pertussis-like toxin subunit: “Structure of typhoid toxin”. X-ray diffraction, 7 pockets (best druggability 0.76). MolNFT v1 #97195 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4K6L
- Type
- protein
- Length
- 1,041 residues
- Chains
- 7
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative pertussis-like toxin subunit; Cytolethal distending toxin subunit B homolog
- EC
- 3.1.-.-, 2.4.2.-
- UniProt
- Q8Z6A3, Q8Z6A7, Q8Z6A4
- Pockets
- 7 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 21% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | Putative pertussis-like toxin subunit | protein | 114 | 20% helix, 43% strand | Q8Z6A3 |
| F | Cytolethal distending toxin subunit B homolog (EC 3.1.-.-) | protein | 247 | 17% helix, 32% strand | Q8Z6A7 |
| G | Putative pertussis-like toxin subunit (EC 2.4.2.-) | protein | 224 | 26% helix, 25% strand | Q8Z6A4 |
Ligands and binding sites
- GOL · Glycerol · additive · 8 copies · chains A, B, D, C, G, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 233 | 0.76 | 0.90 | 37 | GOL |
| 2 | 447 | 0.74 | 0.84 | 67 | empty |
| 3 | 633 | 0.68 | 0.77 | 58 | empty |
| 4 | 227 | 0.63 | 0.82 | 36 | GOL |
| 5 | 236 | 0.59 | 0.80 | 29 | empty |
Interfaces
11 interfaces between chains.
- A–C · 1134 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 1089 Ų buried · 24 hydrogen bonds · protein-protein
- B–D · 1087 Ų buried · 24 hydrogen bonds · protein-protein
- D–E · 1073 Ų buried · 23 hydrogen bonds · protein-protein
- C–E · 1071 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
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 Q8Z6A3
- Every structure of UniProt Q8Z6A7
- Every structure of UniProt Q8Z6A4
- Elsewhere: RCSB PDB 4K6L · PDBe 4K6L · UniProt Q8Z6A3 · UniProt Q8Z6A7 · UniProt Q8Z6A4
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