Research workbench
Crystal structure of the complex between shiga toxin STX2 B subunit and neutralising NB113
Analyse Crystal structure of the complex between shiga toxin STX2 B subunit and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6FE4
- Type
- protein
- Length
- 940 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Shiga-like toxin 2 subunit B; NB113
- UniProt
- P09386
- Pockets
- 8 · best druggability 0.80
Structure
x-ray diffraction · 6 distinct chains · 11% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Shiga-like toxin 2 subunit B | protein | 72 | 15% helix, 43% strand | P09386 |
| B, C, E | Shiga-like toxin 2 subunit B | protein | 71 | 15% helix, 46% strand | P09386 |
| D | Shiga-like toxin 2 subunit B | protein | 70 | 16% helix, 47% strand | P09386 |
| F, H | NB113 | protein | 117 | 8% helix, 50% strand | — |
| G, J | NB113 | protein | 116 | 8% helix, 50% strand | — |
| I | NB113 | protein | 119 | 8% helix, 50% strand | — |
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1081 | 0.80 | 0.81 | 122 | empty |
| 2 | 952 | 0.74 | 0.77 | 45 | empty |
| 3 | 306 | 0.54 | 0.75 | 44 | empty |
| 4 | 262 | 0.51 | 0.75 | 37 | empty |
| 5 | 128 | 0.42 | 0.76 | 19 | empty |
Interfaces
20 interfaces between chains.
- A–B · 728 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 724 Ų buried · 14 hydrogen bonds · protein-protein
- D–E · 718 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 716 Ų buried · 12 hydrogen bonds · protein-protein
- A–E · 716 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 6FE4 · Crystal structure of the complex between Shiga toxin Stx2 B subunit and neutralising Nb113 · 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 P09386
- Elsewhere: RCSB PDB 6FE4 · PDBe 6FE4 · UniProt P09386
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