Research workbench
Crystal structure of a mouse MHC class I protein, H2-db, in complex with a mutated peptide (R7A) of the influenza a acid polymerase
Analyse Crystal structure of a mouse MHC class I protein, H2-db, in complex with a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1YN7
- Type
- protein
- Length
- 383 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- H-2 class I histocompatibility antigen, D-B alpha chain; Beta-2-microglobulin; 10-mer…
- EC
- 2.7.7.48
- UniProt
- P01899, P01887, P13175
- Pockets
- 3 · best druggability 0.65
Structure
x-ray diffraction · 3 distinct chains · 19% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | H-2 class I histocompatibility antigen, D-B alpha chain | protein | 273 | 27% helix, 40% strand | P01899 |
| B | Beta-2-microglobulin | protein | 100 | 0% helix, 49% strand | P01887 |
| C | 10-mer peptide from RNA-directed RNA polymerase subunit P2 (EC 2.7.7.48) | protein | 10 | 0% helix, 0% strand | P13175 |
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 544 | 0.65 | 0.76 | 48 | empty |
| 2 | 171 | 0.53 | 0.79 | 35 | empty |
| 3 | 96 | 0.47 | 0.81 | 16 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1290 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 910 Ų buried · 27 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 1YN7 · Crystal structure of a mouse MHC class I protein, H2-Db, in complex with a mutated… · the same entry in another collection · chain A against A, TM-score 1.00
- P01887 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P01887) · 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 P01899
- Every structure of UniProt P01887
- Every structure of UniProt P13175
- Elsewhere: RCSB PDB 1YN7 · PDBe 1YN7 · UniProt P01899 · UniProt P01887 · UniProt P13175
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