MolNFT v1 · #182251 · protein
Crystal structure of HLA-A*03:01 in complex with vvrpsvask, an 9-mer epitope from influenza B virus
7MLE · HLA class I histocompatibility antigen, a alpha chain: “Crystal structure of HLA-A*03:01 in complex with vvrpsvask, an 9-mer epitope from influenza B virus”. X-ray diffraction, 1 ligand (SO4), 4 pockets (best druggability 0.70).…
- PDB
- 7MLE
- Type
- protein
- Length
- 386 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HLA class I histocompatibility antigen, a alpha chain; Beta-2-microglobulin…
- UniProt
- P04439, P61769, P13884
- Ligands
- SO4
- Pockets
- 4 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 17% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HLA class I histocompatibility antigen, a alpha chain | protein | 277 | 24% helix, 39% strand | P04439 |
| B | Beta-2-microglobulin | protein | 100 | 0% helix, 49% strand | P61769 |
| C | Nucleoprotein peptide | protein | 9 | 0% helix, 0% strand | P13884 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
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 | 707 | 0.70 | 0.77 | 65 | empty |
| 2 | 96 | 0.46 | 0.80 | 24 | SO4 |
| 3 | 103 | 0.41 | 0.77 | 19 | SO4 |
| 4 | 52 | 0.28 | 0.74 | 15 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1324 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 864 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 7MLE · Crystal Structure of HLA-A*03:01 in complex with VVRPSVASK, an 9-mer epitope from… · 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 0.99
- 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 0.97
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 P04439
- Every structure of UniProt P61769
- Every structure of UniProt P13884
- Elsewhere: RCSB PDB 7MLE · PDBe 7MLE · UniProt P04439 · UniProt P61769 · UniProt P13884
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