Research workbench
Crystal structure of HLA-A*2402 in complex with avian influenza A(H7N9) virus-derived peptide H7-25 (data set 1)
Analyse Crystal structure of HLA-A*2402 in complex with avian influenza A(H7N9)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5WXD
- Type
- protein
- Length
- 385 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HLA class I histocompatibility antigen, a-24 alpha chain; Beta-2-microglobulin; H7-25
- UniProt
- P05534, P61769
- Pockets
- 3 · best druggability 0.71
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-24 alpha chain | protein | 274 | 26% helix, 41% strand | P05534 |
| B | Beta-2-microglobulin | protein | 100 | 0% helix, 49% strand | P61769 |
| E | H7-25 | protein | 11 | 0% helix, 0% strand | — |
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 599 | 0.71 | 0.79 | 55 | empty |
| 2 | 193 | 0.51 | 0.77 | 37 | empty |
| 3 | 85 | 0.37 | 0.76 | 14 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1444 Ų buried · 15 hydrogen bonds · protein-protein
- A–E · 993 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 5WXD · Crystal Structure of HLA-A*2402 in complex with avian influenza A(H7N9) virus-derived… · 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
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 P05534
- Every structure of UniProt P61769
- Elsewhere: RCSB PDB 5WXD · PDBe 5WXD · UniProt P05534 · UniProt P61769
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