Research workbench
Porcine E.COLI heat-labile enterotoxin B-pentamer in complex with lacto-N-neohexaose
Analyse Porcine E.COLI heat-labile enterotoxin B-pentamer in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6IAL
- Type
- protein
- Length
- 1,014 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Heat-labile enterotoxin B chain
- UniProt
- P32890
- Ligands
- GAL, NAG, BGC, NA, CA
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 24% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D, A | Heat-labile enterotoxin B chain | protein | 100 | 24% helix, 38% strand | P32890 |
| E, F, H, B, C, J | Heat-labile enterotoxin B chain | protein | 103 | 23% helix, 38% strand | P32890 |
| G | Heat-labile enterotoxin B chain | protein | 97 | 25% helix, 38% strand | P32890 |
| I | Heat-labile enterotoxin B chain | protein | 99 | 24% helix, 36% strand | P32890 |
Ligands and binding sites
- GAL · beta-D-galactopyranose · sugar · 6 copies · chains H, J
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains H, J
- BGC · beta-D-glucopyranose · sugar · 2 copies
- NA · Sodium ion · metal · 14 copies · chains D, B, C, E, F, A, G, J, H, I
- CA · Calcium ion · metal · chains B, C
- GOL · Glycerol · additive · 2 copies · chains D, H, B, C
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 | 331 | 0.79 | 0.90 | 58 | NA |
| 2 | 749 | 0.76 | 0.81 | 39 | empty |
| 3 | 368 | 0.71 | 0.83 | 21 | empty |
| 4 | 288 | 0.71 | 0.85 | 45 | NA |
| 5 | 85 | 0.61 | 0.89 | 21 | empty |
Interfaces
25 interfaces between chains.
- B–C · 1349 Ų buried · 21 hydrogen bonds · protein-protein
- A–J · 1291 Ų buried · 22 hydrogen bonds · protein-protein
- I–J · 1281 Ų buried · 22 hydrogen bonds · protein-protein
- D–H · 1269 Ų buried · 25 hydrogen bonds · protein-protein
- C–I · 1257 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 6IAL · Porcine E.coli heat-labile enterotoxin B-pentamer in complex with Lacto-N-neohexaose · the same entry in another collection · chain J against J, TM-score 1.00
- P32890 · AlphaFold monomer V2.0 prediction for heat-labile enterotoxin B chain (P32890) · a predicted model of the same protein · chain D 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 P32890
- Elsewhere: RCSB PDB 6IAL · PDBe 6IAL · UniProt P32890
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