Research workbench
X-ray crystal structure of the lectin-like natural killer cell receptor ly-49C bound to its MHC class I ligand H-2KB
Analyse X-ray crystal structure of the lectin-like natural killer cell receptor ly-49C… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1P1Z
- Type
- protein
- Length
- 478 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, P01887, P01012, Q64329
- Pockets
- 10 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 18% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | H-2 class I histocompatibility antigen, K-B alpha chain | protein | 255 | 24% helix, 35% strand | P01901 |
| B | Beta-2-microglobulin | protein | 97 | 0% helix, 43% strand | P01887 |
| P | Ovalbumin peptide | protein | 8 | 0% helix, 0% strand | P01012 |
| D | LY49-C antigen | protein | 118 | 19% helix, 36% strand | Q64329 |
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1028 | 0.83 | 0.84 | 87 | empty |
| 2 | 224 | 0.56 | 0.78 | 39 | empty |
| 3 | 67 | 0.54 | 0.87 | 20 | empty |
| 4 | 99 | 0.44 | 0.79 | 24 | empty |
| 5 | 153 | 0.42 | 0.74 | 24 | empty |
Interfaces
4 interfaces between chains.
- A–D · 1195 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 1164 Ų buried · 16 hydrogen bonds · protein-protein
- A–P · 833 Ų buried · 15 hydrogen bonds · protein-protein
- B–D · 379 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide (disulfide).
Compared structures
- 1P1Z · X-RAY CRYSTAL STRUCTURE OF THE LECTIN-LIKE NATURAL KILLER CELL RECEPTOR LY-49C BOUND TO… · the same entry in another collection · chain A against A, TM-score 1.00
- P01887 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P01887) · a predicted model of the same protein · chain B against A, TM-score 0.97
- Q64329 · AlphaFold monomer V2.0 prediction for killer cell lectin-like receptor 3 (Q64329) · a predicted model of the same protein · chain D against A, TM-score 0.95
- P01012 · AlphaFold monomer V2.0 prediction for ovalbumin (P01012) · a predicted model of the same protein · chain P against A, TM-score 0.41
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 P01887
- Every structure of UniProt P01012
- Every structure of UniProt Q64329
- Elsewhere: RCSB PDB 1P1Z · PDBe 1P1Z · UniProt P01901 · UniProt P01887 · UniProt P01012 · UniProt Q64329
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