Research workbench
Manipulating the coupled folding and binding process drives affinity maturation in a protein-protein complex
Analyse Manipulating the coupled folding and binding process drives affinity maturation… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3BYY
- Type
- protein
- Length
- 343 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- T cell receptor beta chain 8.2; Enterotoxin type C-3
- UniProt
- P0A0L5
- Ligands
- SO4
- Pockets
- 2 · best druggability 0.57
Structure
x-ray diffraction · 2 distinct chains · 13% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | T cell receptor beta chain 8.2 | protein | 109 | 3% helix, 54% strand | — |
| B | Enterotoxin type C-3 | protein | 234 | 18% helix, 35% strand | P0A0L5 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 245 | 0.57 | 0.78 | 30 | SO4 |
| 2 | 117 | 0.55 | 0.83 | 30 | empty |
Interfaces
1 interface between chains.
- A–B · 689 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 3BYY · Manipulating the coupled folding and binding process drives affinity maturation in a… · the same entry in another collection · chain A against A, TM-score 1.00
- P0A0L5 · AlphaFold monomer V2.0 prediction for enterotoxin type C-3 (P0A0L5) · a predicted model of the same protein · chain B against A, TM-score 0.97
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 P0A0L5
- Elsewhere: RCSB PDB 3BYY · PDBe 3BYY · UniProt P0A0L5
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