MolNFT v1 · #3731 · protein
Mutated shiga-like toxin B subunit (W34A) complexed with receptor GB3 analogue
1D1I · Shiga toxin B-chain: “Mutated shiga-like toxin B subunit (W34A) complexed with receptor GB3 analogue”. X-ray diffraction, 3 ligands (GAL, GLA, BGC), 1 pocket (best druggability 0.71). MolNFT v1 #3731 on GenesisL1: 3D structure…
- PDB
- 1D1I
- Type
- protein
- Length
- 345 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Shiga toxin B-chain
- UniProt
- P08027
- Ligands
- GAL, GLA, BGC
- Pockets
- 1 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 17% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | Shiga toxin B-chain | protein | 69 | 17% helix, 45% strand | P08027 |
Ligands and binding sites
- GAL · beta-D-galactopyranose · sugar · 6 copies · chains A, B, C, D, E
- GLA · alpha-D-galactopyranose · sugar · 6 copies · chains A, B, C, D, E
- BGC · beta-D-glucopyranose · sugar · 5 copies · chains A, B, C, D, E
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 | 775 | 0.71 | 0.77 | 45 | empty |
Interfaces
5 interfaces between chains.
- A–E · 650 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 650 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 649 Ų buried · 12 hydrogen bonds · protein-protein
- D–E · 649 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 647 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 1D1I · Mutated shiga-like toxin B subunit (W34A) complexed with receptor GB3 analogue · 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 P08027
- Elsewhere: RCSB PDB 1D1I · PDBe 1D1I · UniProt P08027
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