Research workbench
Escherichia COLI heat labile enterotoxin type iib B-pentamer complexed with sialylated sugar
Analyse Escherichia COLI heat labile enterotoxin type iib B-pentamer complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5G3L
- Type
- protein
- Length
- 491 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Heat-labile enterotoxin iib, B chain
- UniProt
- P43529
- Ligands
- SIA, GAL, NA
- Pockets
- 1 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 26% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | Heat-labile enterotoxin iib, B chain | protein | 99 | 26% helix, 38% strand | P43529 |
| E, H | Heat-labile enterotoxin iib, B chain | protein | 98 | 27% helix, 39% strand | P43529 |
| F, G | Heat-labile enterotoxin iib, B chain | protein | 98 | 27% helix, 39% strand | P43529 |
Ligands and binding sites
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 5 copies · chains D, E, G, H, F
- GAL · beta-D-galactopyranose · sugar · 3 copies · chains E, G, H, D
- NA · Sodium ion · metal · 4 copies · chains D, E, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1026 | 0.75 | 0.77 | 75 | empty |
Interfaces
5 interfaces between chains.
- D–E · 1214 Ų buried · 16 hydrogen bonds · protein-protein
- G–H · 1198 Ų buried · 14 hydrogen bonds · protein-protein
- E–F · 1180 Ų buried · 14 hydrogen bonds · protein-protein
- D–H · 1179 Ų buried · 14 hydrogen bonds · protein-protein
- F–G · 1157 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide, 3 modified (disulfide, nonstandard).
Compared structures
- 5G3L · Escherichia COLI heat labile enterotoxin type iib B-pentamer complexed with sialylated… · the same entry in another collection · chain H against H, TM-score 1.00
- P43529 · AlphaFold monomer V2.0 prediction for heat-labile enterotoxin iib, B chain (P43529) · a predicted model of the same protein · chain G 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 P43529
- Elsewhere: RCSB PDB 5G3L · PDBe 5G3L · UniProt P43529
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