Research workbench
Crystal structure of HLA A*2402 in complex with tyqwvlknl, an 9-mer epitope from influenza B virus
Analyse Crystal structure of HLA A*2402 in complex with tyqwvlknl, an 9-mer epitope… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6XQA
- Type
- protein
- Length
- 768 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MHC class I antigen; Beta-2-microglobulin; PB2-549-557 peptide from influenza B, tyqwvlknl
- UniProt
- A0A411J078, P61769
- Ligands
- MG
- Pockets
- 9 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 19% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | MHC class I antigen | protein | 276 | 26% helix, 40% strand | A0A411J078 |
| B, E | Beta-2-microglobulin | protein | 99 | 0% helix, 49% strand | P61769 |
| C, F | PB2-549-557 peptide from influenza B, tyqwvlknl | protein | 9 | 0% helix, 0% strand | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1194 | 0.76 | 0.79 | 103 | empty |
| 2 | 576 | 0.68 | 0.78 | 51 | empty |
| 3 | 580 | 0.67 | 0.77 | 56 | empty |
| 4 | 210 | 0.52 | 0.77 | 25 | empty |
| 5 | 93 | 0.41 | 0.78 | 23 | empty |
Interfaces
7 interfaces between chains.
- D–E · 1358 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 1353 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 968 Ų buried · 20 hydrogen bonds · protein-protein
- D–F · 965 Ų buried · 20 hydrogen bonds · protein-protein
- B–D · 173 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 6XQA · Crystal Structure of HLA A*2402 in complex with TYQWVLKNL, an 9-mer epitope from… · the same entry in another collection · chain F against F, 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 0.99
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 A0A411J078
- Every structure of UniProt P61769
- Elsewhere: RCSB PDB 6XQA · PDBe 6XQA · UniProt A0A411J078 · UniProt P61769
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