Research workbench
Crystal structure of the a-subunit of the AB5 toxin from E. COLI with NEU5GC-2,3GAL-1,3GLCNAC
Analyse Crystal structure of the a-subunit of the AB5 toxin from E. COLI with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3DWQ
- Type
- protein
- Length
- 586 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Subtilase cytotoxin, subunit B
- UniProt
- Q3ZTX8
- Ligands
- NGA, GAL, NGC, AZI
- Pockets
- 2 · best druggability 0.67
Structure
x-ray diffraction · 3 distinct chains · 20% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Subtilase cytotoxin, subunit B | protein | 116 | 20% helix, 41% strand | Q3ZTX8 |
| B, D | Subtilase cytotoxin, subunit B | protein | 117 | 20% helix, 40% strand | Q3ZTX8 |
| C | Subtilase cytotoxin, subunit B | protein | 120 | 19% helix, 40% strand | Q3ZTX8 |
Ligands and binding sites
- NGA · 2-acetamido-2-deoxy-beta-D-galactopyranose · sugar · 4 copies · chains A, C, D, E
- GAL · beta-D-galactopyranose · sugar · 4 copies · chains A, C, D, E
- NGC · N-glycolyl-alpha-neuraminic acid · sugar · 4 copies · chains A, C, D, E
- AZI · Azide ion · ion · 4 copies · chains A, E
- 1PE · Pentaethylene glycol · additive · 5 copies · chains A, C, E, B, D
- POL · N-propanol · additive · 4 copies
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 838 | 0.67 | 0.74 | 48 | 1PE |
| 2 | 58 | 0.26 | 0.73 | 10 | empty |
Interfaces
5 interfaces between chains.
- A–E · 1053 Ų buried · 23 hydrogen bonds · protein-protein
- B–D · 1052 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 1044 Ų buried · 21 hydrogen bonds · protein-protein
- B–E · 1042 Ų buried · 27 hydrogen bonds · protein-protein
- C–D · 1039 Ų buried · 25 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide (disulfide).
Compared structures
- 3DWQ · Crystal structure of the A-subunit of the AB5 toxin from E. coli with… · 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 Q3ZTX8
- Elsewhere: RCSB PDB 3DWQ · PDBe 3DWQ · UniProt Q3ZTX8
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