Research workbench
Crystal structure of HLA-CW4, a ligand for the KIR2D natural killer cell inhibitory receptor
Analyse Crystal structure of HLA-CW4, a ligand for the KIR2D 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
- 1QQD
- Type
- protein
- Length
- 381 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histocompatibility leukocyte antigen (HLA)-CW4 (heavy chain); Beta-2 microglobulin…
- UniProt
- P30504, P61769
- Pockets
- 4 · best druggability 0.67
Structure
x-ray diffraction · 3 distinct chains · 20% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histocompatibility leukocyte antigen (HLA)-CW4 (heavy chain) | protein | 273 | 28% helix, 39% strand | P30504 |
| B | Beta-2 microglobulin | protein | 99 | 0% helix, 47% strand | P61769 |
| C | HLA-CW4 specific peptide | protein | 9 | 0% helix, 0% strand | — |
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 583 | 0.67 | 0.77 | 54 | empty |
| 2 | 155 | 0.46 | 0.76 | 23 | empty |
| 3 | 132 | 0.44 | 0.77 | 25 | empty |
| 4 | 52 | 0.35 | 0.79 | 14 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1282 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 973 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 1QQD · Crystal structure of HLA-CW4, a ligand for the KIR2D natural killer cell inhibitory… · the same entry in another collection · chain A against A, TM-score 1.00
- P61769 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P61769) · 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 P30504
- Every structure of UniProt P61769
- Elsewhere: RCSB PDB 1QQD · PDBe 1QQD · UniProt P30504 · UniProt P61769
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