MolNFT v1 · #151607 · protein
Engineered higher-order assembly of cholera toxin B subunits via the addition of C-terminal parallel coiled-coiled domains
6HSV: “Engineered higher-order assembly of cholera toxin B subunits via the addition of C-terminal parallel…”. X-ray diffraction, 2 ligands (PO4, CL), 20 pockets (best druggability 0.75). MolNFT v1 #151607 on GenesisL1: 3D structure…
- PDB
- 6HSV
- Type
- protein
- Length
- 2,237 residues
- Chains
- 20
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Toxin B subunit
- UniProt
- Q7X2D2
- Ligands
- PO4, CL
- Pockets
- 20 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 24% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, H, R | Toxin B subunit | protein | 104 | 22% helix, 36% strand | Q7X2D2 |
| B, D, I, K, Q, S, T | Toxin B subunit | protein | 103 | 23% helix, 37% strand | Q7X2D2 |
| C | Toxin B subunit | protein | 97 | 24% helix, 38% strand | Q7X2D2 |
| E, F, G, J, L, M, N, O, P | Toxin B subunit | protein | 123 | 27% helix, 30% strand | Q7X2D2 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 6 copies · chains A, D, F, I, P, Q
- CL · Chloride ion · ion · chains T
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 27 copies · chains A, E, B, C, D, G, H, F, I, J, K, L, M, N, O, P, Q, T, R, S
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1050 | 0.75 | 0.78 | 44 | empty |
| 2 | 1097 | 0.75 | 0.78 | 44 | empty |
| 3 | 1174 | 0.75 | 0.77 | 58 | empty |
| 4 | 1058 | 0.74 | 0.77 | 46 | empty |
| 5 | 151 | 0.70 | 0.90 | 30 | empty |
Interfaces
29 interfaces between chains.
- F–G · 1557 Ų buried · 26 hydrogen bonds · protein-protein
- N–O · 1523 Ų buried · 24 hydrogen bonds · protein-protein
- L–M · 1516 Ų buried · 23 hydrogen bonds · protein-protein
- H–I · 1405 Ų buried · 25 hydrogen bonds · protein-protein
- R–S · 1382 Ų buried · 27 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 disulfide (disulfide).
Compared structures
- 6HSV · Engineered higher-order assembly of Cholera Toxin B subunits via the addition of… · the same entry in another collection · chain A against A, 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 Q7X2D2
- Elsewhere: RCSB PDB 6HSV · PDBe 6HSV · UniProt Q7X2D2
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