MolNFT v1 · #126325 · protein
Cholera toxin el tor B-pentamer in complex with inhibitor PC262
5LZG · Cholera enterotoxin subunit B: “Cholera toxin el tor B-pentamer in complex with inhibitor PC262”. X-ray diffraction, 1 ligand (7BN), 10 pockets (best druggability 0.75). MolNFT v1 #126325 on GenesisL1: 3D structure, binding sites…
- PDB
- 5LZG
- 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
- 7BN
- Pockets
- 10 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 22% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | Cholera enterotoxin subunit B | protein | 103 | 22% helix, 37% strand | P01556 |
Ligands and binding sites
- 7BN · (2~{R},4~{S},5~{R},6~{R})-5-acetamido-2-[4-[3-[2-[(2~{S},3~{R},4~{R},5~{R},6~{R})-6-(hydroxymethyl)-3, 4,5-tris(oxidanyl)oxan-2-yl]ethylamino]-3-oxidanylidene-propyl]-1,2,3-triazol-1-yl]-4-oxidanyl-6-[(1~{R},2~{R})-1,2,3-tris(oxidanyl)propyl]oxane-2-carboxylic acid · ligand · 5 copies · chains A, B, C, D, E
- IMD · Imidazole · additive · 2 copies · chains A, D
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A, E
- PEG · Di(hydroxyethyl)ether · additive · chains C
- MRD · (4R)-2-methylpentane-2,4-diol · additive · chains D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1042 | 0.75 | 0.78 | 43 | empty |
| 2 | 53 | 0.41 | 0.83 | 16 | empty |
| 3 | 56 | 0.37 | 0.80 | 19 | empty |
| 4 | 51 | 0.37 | 0.80 | 18 | empty |
| 5 | 70 | 0.34 | 0.76 | 15 | empty |
Interfaces
5 interfaces between chains.
- B–C · 1305 Ų buried · 22 hydrogen bonds · protein-protein
- D–E · 1298 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 1295 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 1290 Ų buried · 22 hydrogen bonds · protein-protein
- A–E · 1277 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 5LZG · Cholera toxin El Tor B-pentamer in complex with inhibitor PC262 · 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 B 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 5LZG · PDBe 5LZG · UniProt P01556
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