MolNFT v1 · #138860 · protein
Crystal structure of HLA-A*2402 in complex with 2009 pandemic influenza A(H1N1) virus and avian influenza A(H5N1) virus-derived peptide H1-25
5WWU · HLA class I histocompatibility antigen, a-24 alpha chain: “Crystal structure of HLA-A*2402 in complex with 2009 pandemic influenza A(H1N1) virus and avian influenza…”. X-ray diffraction, 5 pockets (best druggability 0.70). MolNFT v1…
- PDB
- 5WWU
- Type
- protein
- Length
- 384 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…
- UniProt
- P05534, P61769
- Pockets
- 5 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 18% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HLA class I histocompatibility antigen, a-24 alpha chain | protein | 274 | 26% helix, 40% strand | P05534 |
| B | Beta-2-microglobulin | protein | 99 | 0% helix, 49% strand | P61769 |
| E | Leu-tyr-lys-lys-leu-lys-arg-glu-ile-thr-phe | protein | 11 | 0% helix, 0% strand | — |
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 583 | 0.70 | 0.79 | 52 | empty |
| 2 | 135 | 0.47 | 0.78 | 29 | empty |
| 3 | 86 | 0.42 | 0.79 | 16 | empty |
| 4 | 73 | 0.39 | 0.79 | 23 | empty |
| 5 | 52 | 0.29 | 0.76 | 16 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1371 Ų buried · 20 hydrogen bonds · protein-protein
- A–E · 1004 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 5WWU · Crystal Structure of HLA-A*2402 in complex with 2009 pandemic influenza A(H1N1) virus and… · 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 5WWU · PDBe 5WWU · UniProt P05534 · UniProt P61769
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