Research workbench
Crystal structure of HLA-A3*01 in complex with a wild-type beta- catenin peptide
Analyse Crystal structure of HLA-A3*01 in complex with a wild-type beta- catenin peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6O9B
- Type
- protein
- Length
- 388 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HLA class I histocompatibility antigen, a-3 alpha chain; Beta-2-microglobulin; Catenin…
- UniProt
- P04439, P61769, P35222
- Pockets
- 4 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 18% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HLA class I histocompatibility antigen, a-3 alpha chain | protein | 278 | 25% helix, 41% strand | P04439 |
| B | Beta-2-microglobulin | protein | 101 | 0% helix, 49% strand | P61769 |
| C | Catenin beta-1 | protein | 9 | 0% helix, 0% strand | P35222 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 7 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 4 copies · chains A, B
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 3 copies · chains A, B
- PG4 · Tetraethylene glycol · additive · 2 copies · chains A, B
- IMD · Imidazole · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 694 | 0.72 | 0.79 | 65 | IMD, PEG, EDO, PG4, MES |
| 2 | 100 | 0.46 | 0.80 | 20 | PG4 |
| 3 | 85 | 0.46 | 0.81 | 19 | PEG |
| 4 | 52 | 0.35 | 0.79 | 15 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1473 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 863 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 6O9B · Crystal structure of HLA-A3*01 in complex with a wild-type beta-catenin peptide · the same entry in another collection · chain A against A, TM-score 1.00
- P61769 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P61769) · a predicted model of the same protein · chain B against A, TM-score 0.98
- P04439 · AlphaFold monomer V2.0 prediction for HLA class I histocompatibility antigen, a alpha… · a predicted model of the same protein · chain A against A, TM-score 0.96
- P35222 · AlphaFold monomer V2.0 prediction for catenin beta-1 (P35222) · a predicted model of the same protein · chain C against A, TM-score 0.41
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 P04439
- Every structure of UniProt P61769
- Every structure of UniProt P35222
- Elsewhere: RCSB PDB 6O9B · PDBe 6O9B · UniProt P04439 · UniProt P61769 · UniProt P35222
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