Research workbench
Recognition of the MHC class ib molecule H2-Q10 by the natural killer cell receptor LY49C
Analyse Recognition of the MHC class ib molecule H2-Q10 by the natural killer cell… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5J6H
- Type
- protein
- Length
- 382 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- H-2 class I histocompatibility antigen, Q10 alpha chain; Beta-2-microglobulin…
- UniProt
- P01898, P01887
- Ligands
- NCA, NA
- Pockets
- 4 · best druggability 0.67
Structure
x-ray diffraction · 3 distinct chains · 18% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | H-2 class I histocompatibility antigen, Q10 alpha chain | protein | 275 | 25% helix, 39% strand | P01898 |
| B | Beta-2-microglobulin | protein | 99 | 0% helix, 49% strand | P01887 |
| F | Val-gly-ile-thr-asn-val-asp-leu | protein | 8 | 0% helix, 0% strand | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 580 | 0.67 | 0.77 | 58 | empty |
| 2 | 170 | 0.52 | 0.78 | 29 | empty |
| 3 | 55 | 0.40 | 0.82 | 18 | empty |
| 4 | 55 | 0.33 | 0.77 | 14 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1234 Ų buried · 21 hydrogen bonds · protein-protein
- A–F · 783 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 5J6H · Recognition of the MHC class Ib molecule H2-Q10 by the natural killer cell receptor Ly49C · the same entry in another collection · chain A against A, TM-score 1.00
- P01898 · AlphaFold monomer V2.0 prediction for H-2 class I histocompatibility antigen, Q10 alpha… · a predicted model of the same protein · chain A against A, TM-score 0.99
- 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 P01898
- Every structure of UniProt P01887
- Elsewhere: RCSB PDB 5J6H · PDBe 5J6H · UniProt P01898 · UniProt P01887
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