MolNFT v1 · #126328 · protein
Cholera toxin el tor B-pentamer in complex with inhibitor LAURA237
5LZJ · Cholera enterotoxin subunit B: “Cholera toxin el tor B-pentamer in complex with inhibitor LAURA237”. X-ray diffraction, 2 ligands (7BT, SO4), 9 pockets (best druggability 0.74). MolNFT v1 #126328 on GenesisL1: 3D structure, binding…
- PDB
- 5LZJ
- Type
- protein
- Length
- 515 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cholera enterotoxin subunit B
- UniProt
- P01556
- Ligands
- 7BT, SO4
- Pockets
- 9 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 25% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | Cholera enterotoxin subunit B | protein | 103 | 25% helix, 37% strand | P01556 |
Ligands and binding sites
- 7BT · (~{Z})-~{N}-[2-[(2~{R},3~{R},4~{R},5~{R},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]ethyl]-3-(3,4,5-trimethoxyphenyl)prop-2-enamide · ligand · 2 copies · chains C, D
- SO4 · Sulfate ion · ion · chains A
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains B, C, D, E
- PGE · Triethylene glycol · additive · 2 copies · chains B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1166 | 0.74 | 0.77 | 44 | empty |
| 2 | 58 | 0.47 | 0.85 | 19 | empty |
| 3 | 52 | 0.42 | 0.83 | 19 | empty |
| 4 | 56 | 0.41 | 0.82 | 19 | empty |
| 5 | 51 | 0.36 | 0.80 | 13 | empty |
Interfaces
5 interfaces between chains.
- D–E · 1325 Ų buried · 22 hydrogen bonds · protein-protein
- B–C · 1281 Ų buried · 25 hydrogen bonds · protein-protein
- C–D · 1279 Ų buried · 21 hydrogen bonds · protein-protein
- A–E · 1260 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1242 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 5LZJ · Cholera toxin El Tor B-pentamer in complex with inhibitor Laura237 · the same entry in another collection · chain E against E, TM-score 1.00
- P01556 · AlphaFold monomer V2.0 prediction for cholera enterotoxin subunit B (P01556) · a predicted model of the same protein · chain C against A, TM-score 0.99
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 P01556
- Elsewhere: RCSB PDB 5LZJ · PDBe 5LZJ · UniProt P01556
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