MolNFT v1 · #60782 · protein
Crystal structure of ha-1 minor histocompatibility antigen bound to human class I MHC HLA-A2
3D25 · HLA class I histocompatibility antigen, a-2 alpha chain: “Crystal structure of ha-1 minor histocompatibility antigen bound to human class I MHC HLA-A2”. X-ray diffraction, 5 pockets (best druggability 0.67). MolNFT v1 #60782 on…
- PDB
- 3D25
- Type
- protein
- Length
- 381 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HLA class I histocompatibility antigen, a-2 alpha chain; Beta-2-microglobulin; Nonameric…
- UniProt
- P01892, P61769, Q6P189
- Pockets
- 5 · best druggability 0.67
Structure
x-ray diffraction · 3 distinct chains · 20% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HLA class I histocompatibility antigen, a-2 alpha chain | protein | 274 | 27% helix, 40% strand | P01892 |
| B | Beta-2-microglobulin | protein | 98 | 0% helix, 50% strand | P61769 |
| C | Nonameric peptide from ha-1 | protein | 9 | 0% helix, 0% strand | Q6P189 |
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 | 516 | 0.67 | 0.78 | 48 | empty |
| 2 | 111 | 0.45 | 0.79 | 23 | empty |
| 3 | 77 | 0.41 | 0.80 | 18 | empty |
| 4 | 96 | 0.34 | 0.74 | 19 | empty |
| 5 | 63 | 0.32 | 0.75 | 14 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1245 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 844 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 3D25 · Crystal structure of HA-1 minor histocompatibility antigen bound to human class I MHC… · 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 P01892
- Every structure of UniProt P61769
- Every structure of UniProt Q6P189
- Elsewhere: RCSB PDB 3D25 · PDBe 3D25 · UniProt P01892 · UniProt P61769 · UniProt Q6P189
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