MolNFT v1 · #31509 · protein
The immunogenicity of a viral cytotoxic T cell epitope is controlled by its MHC-bound conformation
2AXF · HLA class I histocompatibility antigen, B*3508 heavy chain: “The immunogenicity of a viral cytotoxic T cell epitope is controlled by its MHC-bound conformation”. X-ray diffraction, 4 pockets (best druggability 0.67). MolNFT v1…
- PDB
- 2AXF
- 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, B*3508 heavy chain; Beta-2-microglobulin; 10-mer…
- UniProt
- P30685, P61769, P03206
- Pockets
- 4 · best druggability 0.67
Structure
x-ray diffraction · 3 distinct chains · 19% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HLA class I histocompatibility antigen, B*3508 heavy chain | protein | 276 | 27% helix, 40% strand | P30685 |
| B | Beta-2-microglobulin | protein | 99 | 0% helix, 49% strand | P61769 |
| C | 10-mer peptide from BZLF1 trans-activator protein | protein | 10 | 0% helix, 0% strand | P03206 |
Ligands and binding sites
- ACY · Acetic acid · additive · 2 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 610 | 0.67 | 0.77 | 54 | ACY |
| 2 | 185 | 0.52 | 0.78 | 35 | empty |
| 3 | 105 | 0.42 | 0.77 | 24 | ACY |
| 4 | 79 | 0.42 | 0.79 | 16 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1322 Ų buried · 24 hydrogen bonds · protein-protein
- A–C · 858 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 2AXF · The Immunogenicity of a Viral Cytotoxic T Cell Epitope is controlled by its MHC-bound… · 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
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 P30685
- Every structure of UniProt P61769
- Every structure of UniProt P03206
- Elsewhere: RCSB PDB 2AXF · PDBe 2AXF · UniProt P30685 · UniProt P61769 · UniProt P03206
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