MolNFT v1 · #77220 · protein
Crystal structure of staphylococcal enterotoxin B in complex with an affinity matured mouse TCR VBETA8.2 protein, G5-8
3R8B · Enterotoxin type B: “Crystal structure of staphylococcal enterotoxin B in complex with an affinity matured mouse TCR VBETA8.2…”. X-ray diffraction, 3 ligands (ZN, CL, SO4), 20 pockets (best druggability 0.88). MolNFT v1 #77220 on…
- PDB
- 3R8B
- Type
- protein
- Length
- 2,698 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Enterotoxin type B; G5-8
- UniProt
- P01552
- Ligands
- ZN, CL, SO4
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 9 distinct chains · 14% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, K | Enterotoxin type B | protein | 224 | 21% helix, 40% strand | P01552 |
| B, D, L | G5-8 | protein | 114 | 3% helix, 58% strand | — |
| F, H | G5-8 | protein | 113 | 3% helix, 53% strand | — |
| G | Enterotoxin type B | protein | 223 | 21% helix, 41% strand | P01552 |
| I | Enterotoxin type B | protein | 226 | 20% helix, 41% strand | P01552 |
| J | G5-8 | protein | 112 | 3% helix, 50% strand | — |
| M, O | Enterotoxin type B | protein | 225 | 20% helix, 41% strand | P01552 |
| N | G5-8 | protein | 112 | 3% helix, 58% strand | — |
| P | G5-8 | protein | 111 | 3% helix, 54% strand | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 24 copies · chains B, D, F, P, O, E, J, C, L, H, A, N, G, K, M, I
- CL · Chloride ion · ion · 14 copies · chains J, B, D, F, P, L, N, I, A, G, C, M, O
- SO4 · Sulfate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 962 | 0.88 | 0.89 | 116 | CL |
| 2 | 695 | 0.86 | 0.90 | 89 | CL |
| 3 | 471 | 0.76 | 0.84 | 64 | empty |
| 4 | 810 | 0.75 | 0.79 | 86 | empty |
| 5 | 819 | 0.74 | 0.79 | 85 | empty |
Interfaces
34 interfaces between chains.
- F–P · 909 Ų buried · 20 hydrogen bonds · protein-protein
- B–D · 871 Ų buried · 17 hydrogen bonds · protein-protein
- A–O · 838 Ų buried · 5 hydrogen bonds · protein-protein
- C–E · 823 Ų buried · 4 hydrogen bonds · protein-protein
- I–J · 798 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide (disulfide).
Compared structures
- 3R8B · Crystal structure of Staphylococcal Enterotoxin B in complex with an affinity matured… · the same entry in another collection · chain P against P, 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 P01552
- Elsewhere: RCSB PDB 3R8B · PDBe 3R8B · UniProt P01552
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