Research workbench
Cholera toxin classical B-pentamer in complex with a lewis-Y
Analyse Cholera toxin classical B-pentamer in complex with a lewis-Y in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ELD
- Type
- protein
- Length
- 515 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cholera enterotoxin B subunit
- UniProt
- Q57193
- Ligands
- FUC, GAL, NDG, A2G, GLA, NA
- Pockets
- 3 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 22% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | Cholera enterotoxin B subunit | protein | 103 | 22% helix, 36% strand | Q57193 |
Ligands and binding sites
- FUC · alpha-L-fucopyranose · sugar · 8 copies · chains A, E, C, B, D
- GAL · beta-D-galactopyranose · sugar · 7 copies · chains A, C, D, E
- NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar · 4 copies · chains A, E, B, C, D
- A2G · 2-acetamido-2-deoxy-alpha-D-galactopyranose · sugar · 4 copies · chains A, C, D, E
- GLA · alpha-D-galactopyranose · sugar · chains E
- NA · Sodium ion · metal · chains B
- PGE · Triethylene glycol · additive · 3 copies · chains C, D, E
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, D, E
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1146 | 0.74 | 0.77 | 56 | MES |
| 2 | 65 | 0.39 | 0.80 | 21 | empty |
| 3 | 50 | 0.34 | 0.78 | 13 | empty |
Interfaces
5 interfaces between chains.
- B–C · 1324 Ų buried · 24 hydrogen bonds · protein-protein
- C–D · 1315 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 1312 Ų buried · 27 hydrogen bonds · protein-protein
- A–E · 1288 Ų buried · 22 hydrogen bonds · protein-protein
- D–E · 1250 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 5ELD · Cholera toxin classical B-pentamer in complex with A Lewis-y · 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 Q57193
- Elsewhere: RCSB PDB 5ELD · PDBe 5ELD · UniProt Q57193
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