Research workbench
The crystal structure of LY49C bound to H-2KB
Analyse The crystal structure of LY49C bound to H-2KB in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3C8K
- Type
- protein
- Length
- 506 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- H-2 class I histocompatibility antigen, K-B alpha chain; Beta-2 microglobulin; Ovalbumin…
- UniProt
- P01901, Q91XJ8, Q61198
- Pockets
- 8 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 19% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | H-2 class I histocompatibility antigen, K-B alpha chain | protein | 274 | 26% helix, 41% strand | P01901 |
| B | Beta-2 microglobulin | protein | 99 | 0% helix, 49% strand | Q91XJ8 |
| P | Ovalbumin peptide | protein | 8 | 0% helix, 0% strand | — |
| D | Natural killer cell receptor ly-49C | protein | 125 | 21% helix, 36% strand | Q61198 |
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1151 | 0.83 | 0.84 | 93 | empty |
| 2 | 166 | 0.52 | 0.78 | 34 | empty |
| 3 | 107 | 0.50 | 0.81 | 23 | empty |
| 4 | 138 | 0.44 | 0.76 | 22 | empty |
| 5 | 52 | 0.42 | 0.83 | 16 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1230 Ų buried · 23 hydrogen bonds · protein-protein
- A–D · 1048 Ų buried · 17 hydrogen bonds · protein-protein
- A–P · 866 Ų buried · 16 hydrogen bonds · protein-protein
- B–D · 322 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide (disulfide).
Compared structures
- 3C8K · The crystal structure of Ly49C bound to H-2Kb · the same entry in another collection · chain A against A, TM-score 1.00
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 P01901
- Every structure of UniProt Q91XJ8
- Every structure of UniProt Q61198
- Elsewhere: RCSB PDB 3C8K · PDBe 3C8K · UniProt P01901 · UniProt Q91XJ8 · UniProt Q61198
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