Research workbench
Crystal structure of the B-subunit of the AB5 toxin from E. COLI with NEU5GC
Analyse Crystal structure of the B-subunit of the AB5 toxin from E. COLI with NEU5GC in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3DWP
- 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
- NGC
- Pockets
- 1 · best druggability 0.68
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, 42% strand | Q3ZTX8 |
| B, D | Subtilase cytotoxin, subunit B | protein | 117 | 20% helix, 40% strand | Q3ZTX8 |
| C | Subtilase cytotoxin, subunit B | protein | 120 | 19% helix, 39% strand | Q3ZTX8 |
Ligands and binding sites
- NGC · N-glycolyl-alpha-neuraminic acid · sugar · 5 copies · chains A, B, C, D, E
- 1PE · Pentaethylene glycol · additive · 5 copies · chains A, C, E, B, D
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 | 886 | 0.68 | 0.74 | 56 | 1PE |
Interfaces
5 interfaces between chains.
- B–D · 1054 Ų buried · 21 hydrogen bonds · protein-protein
- B–E · 1048 Ų buried · 24 hydrogen bonds · protein-protein
- A–C · 1047 Ų buried · 22 hydrogen bonds · protein-protein
- A–E · 1047 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 1027 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide (disulfide).
Compared structures
- 3DWP · Crystal structure of the B-subunit of the AB5 toxin from E. Coli with Neu5Gc · 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 3DWP · PDBe 3DWP · UniProt Q3ZTX8
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