Research workbench
Complex of a B21 chicken MHC class I molecule and a 11MER chicken peptide
Analyse Complex of a B21 chicken MHC class I molecule and a 11MER chicken peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5AD0
- Type
- protein
- Length
- 378 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MHC class I alpha chain 2; Beta-2-microglobulin; 11MER peptide
- UniProt
- Q95601, P21611
- Ligands
- CA
- Pockets
- 1 · best druggability 0.66
Structure
x-ray diffraction · 3 distinct chains · 20% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MHC class I alpha chain 2 | protein | 269 | 27% helix, 41% strand | Q95601 |
| B | Beta-2-microglobulin | protein | 98 | 0% helix, 51% strand | P21611 |
| C | 11MER peptide | protein | 11 | 36% helix, 0% strand | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 486 | 0.66 | 0.78 | 50 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1635 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 915 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 5AD0 · Complex of a B21 chicken MHC class I molecule and a 11MER chicken peptide · the same entry in another collection · chain A against A, 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 Q95601
- Every structure of UniProt P21611
- Elsewhere: RCSB PDB 5AD0 · PDBe 5AD0 · UniProt Q95601 · UniProt P21611
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