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An immmunodominant ctl epitope from rinderpest virus presented by cattle MHC class I molecule N*01801 (bola-A11)
Analyse An immmunodominant ctl epitope from rinderpest virus presented by cattle MHC… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3PWV
- Type
- protein
- Length
- 762 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MHC class I antigen; Beta-2-microglobulin; 9-mer peptide from hemagglutinin
- UniProt
- Q95477, P01888, Q9YKD7
- Pockets
- 11 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 19% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | MHC class I antigen | protein | 274 | 27% helix, 39% strand | Q95477 |
| B, E | Beta-2-microglobulin | protein | 98 | 0% helix, 50% strand | P01888 |
| C, F | 9-mer peptide from hemagglutinin | protein | 9 | 0% helix, 0% strand | Q9YKD7 |
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 652 | 0.69 | 0.77 | 64 | empty |
| 2 | 566 | 0.67 | 0.77 | 59 | empty |
| 3 | 470 | 0.65 | 0.78 | 49 | empty |
| 4 | 386 | 0.60 | 0.76 | 37 | empty |
| 5 | 157 | 0.46 | 0.76 | 18 | empty |
Interfaces
7 interfaces between chains.
- A–B · 1331 Ų buried · 23 hydrogen bonds · protein-protein
- D–E · 1311 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 891 Ų buried · 18 hydrogen bonds · protein-protein
- D–F · 879 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 686 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 3PWV · An immmunodominant CTL epitope from rinderpest virus presented by cattle MHC class I… · the same entry in another collection · chain F against F, TM-score 1.00
- P01888 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P01888) · a predicted model of the same protein · chain E 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 Q95477
- Every structure of UniProt P01888
- Every structure of UniProt Q9YKD7
- Elsewhere: RCSB PDB 3PWV · PDBe 3PWV · UniProt Q95477 · UniProt P01888 · UniProt Q9YKD7
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