Research workbench
Structure of a complex between the human natural killer cell receptor KIR2DL2 and a class I MHC ligand HLA-CW3
Analyse Structure of a complex between the human natural killer cell receptor KIR2DL2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1EFX
- Type
- protein
- Length
- 781 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HLA-CW3 (heavy chain); Beta-2-microglobulin; Peptide from importin alpha-2; Natural…
- UniProt
- P61769, P52292, P43627
- Pockets
- 9 · best druggability 0.67
Structure
x-ray diffraction · 4 distinct chains · 13% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HLA-CW3 (heavy chain) | protein | 278 | 27% helix, 38% strand | — |
| B | Beta-2-microglobulin | protein | 100 | 0% helix, 46% strand | P61769 |
| C | Peptide from importin alpha-2 | protein | 9 | 0% helix, 0% strand | P52292 |
| D, E | Natural killer cell receptor KIR2DL2 | protein | 197 | 2% helix, 56% strand | P43627 |
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 565 | 0.67 | 0.77 | 58 | empty |
| 2 | 138 | 0.54 | 0.81 | 20 | empty |
| 3 | 126 | 0.43 | 0.76 | 20 | empty |
| 4 | 78 | 0.39 | 0.78 | 22 | empty |
| 5 | 53 | 0.36 | 0.80 | 16 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1346 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 824 Ų buried · 16 hydrogen bonds · protein-protein
- A–D · 750 Ų buried · 14 hydrogen bonds · protein-protein
- D–E · 361 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 115 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 7 disulfide (disulfide).
Compared structures
- 1EFX · Structure of a complex between the human natural killer cell receptor KIR2DL2 and a class… · the same entry in another collection · chain E against E, 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
- P43627 · AlphaFold monomer V2.0 prediction for killer cell immunoglobulin-like receptor 2DL2… · a predicted model of the same protein · chain D against A, TM-score 0.96
- P52292 · AlphaFold monomer V2.0 prediction for importin subunit alpha-1 (P52292) · a predicted model of the same protein · chain C against A, TM-score 0.37
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 P61769
- Every structure of UniProt P52292
- Every structure of UniProt P43627
- Elsewhere: RCSB PDB 1EFX · PDBe 1EFX · UniProt P61769 · UniProt P52292 · UniProt P43627
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