MolNFT v1 · #55602 · protein
Structural features underlying T-cell receptor sensitivity to concealed MHC class I micropolymorphisms
2YPK · HLA class I histocompatibility antigen, B-57 alpha chain: “Structural features underlying T-cell receptor sensitivity to concealed MHC class I micropolymorphisms”. X-ray diffraction, 6 pockets (best druggability 0.69). MolNFT v1…
- PDB
- 2YPK
- 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, B-57 alpha chain; Beta-2-microglobulin; KF11 P24…
- UniProt
- P18465, P61769, Q70XD7
- Pockets
- 6 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 20% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HLA class I histocompatibility antigen, B-57 alpha chain | protein | 274 | 28% helix, 39% strand | P18465 |
| B | Beta-2-microglobulin | protein | 99 | 0% helix, 49% strand | P61769 |
| C | KF11 P24 gag peptide | protein | 11 | 0% helix, 0% strand | Q70XD7 |
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 621 | 0.69 | 0.78 | 52 | empty |
| 2 | 66 | 0.67 | 0.94 | 21 | empty |
| 3 | 89 | 0.45 | 0.80 | 22 | empty |
| 4 | 111 | 0.44 | 0.78 | 20 | empty |
| 5 | 56 | 0.36 | 0.78 | 14 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1275 Ų buried · 29 hydrogen bonds · protein-protein
- A–C · 853 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 2YPK · Structural features underlying T-cell receptor sensitivity to concealed MHC class I… · 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 P18465
- Every structure of UniProt P61769
- Every structure of UniProt Q70XD7
- Elsewhere: RCSB PDB 2YPK · PDBe 2YPK · UniProt P18465 · UniProt P61769 · UniProt Q70XD7
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