Research workbench
Complex of a B2 chicken MHC class I molecule and a 9MER chicken peptide
Analyse Complex of a B2 chicken MHC class I molecule and a 9MER chicken peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4CVX
- Type
- protein
- Length
- 754 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MHC class I alpha chain 2; Beta-2-microglobulin; Self-peptide
- UniProt
- O46789, P21611, Q5ZJG4
- Pockets
- 8 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 19% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | MHC class I alpha chain 2 | protein | 272 | 26% helix, 40% strand | O46789 |
| B, E | Beta-2-microglobulin | protein | 96 | 0% helix, 51% strand | P21611 |
| C, F | Self-peptide | protein | 9 | 0% helix, 0% strand | Q5ZJG4 |
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 443 | 0.71 | 0.81 | 50 | empty |
| 2 | 502 | 0.69 | 0.79 | 53 | empty |
| 3 | 148 | 0.52 | 0.80 | 27 | empty |
| 4 | 113 | 0.43 | 0.77 | 23 | empty |
| 5 | 174 | 0.42 | 0.73 | 27 | empty |
Interfaces
8 interfaces between chains.
- D–E · 1510 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 1510 Ų buried · 9 hydrogen bonds · protein-protein
- D–F · 880 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 874 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 497 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 4CVX · Complex of a B2 chicken MHC class I molecule and a 9MER chicken peptide · the same entry in another collection · chain F against F, TM-score 1.00
- P21611 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P21611) · a predicted model of the same protein · chain B against A, TM-score 0.96
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 O46789
- Every structure of UniProt P21611
- Every structure of UniProt Q5ZJG4
- Elsewhere: RCSB PDB 4CVX · PDBe 4CVX · UniProt O46789 · UniProt P21611 · UniProt Q5ZJG4
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