Research workbench
Crystal structure of the human natural killer cell inhibitory receptor KIR2DL1 bound to its MHC ligand HLA-CW4
Analyse Crystal structure of the human natural killer cell inhibitory receptor KIR2DL1… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1IM9
- Type
- protein
- Length
- 963 residues
- Chains
- 7
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HLA class I histocompatibility antigen, cw-4 CW*0401 alpha chain; Beta-2 microglobulin…
- UniProt
- P30504, P61769, P43626
- Pockets
- 16 · best druggability 0.72
Structure
x-ray diffraction · 4 distinct chains · 14% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | HLA class I histocompatibility antigen, cw-4 CW*0401 alpha chain | protein | 275 | 28% helix, 40% strand | P30504 |
| B, F | Beta-2 microglobulin | protein | 100 | 0% helix, 49% strand | P61769 |
| C, G | HLA-CW4-specific peptide | protein | 9 | 0% helix, 0% strand | — |
| D | Killer cell immunoglobulin-like receptor 2DL1 | protein | 195 | 2% helix, 55% strand | P43626 |
Pockets
16 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 661 | 0.72 | 0.79 | 62 | empty |
| 2 | 514 | 0.67 | 0.78 | 53 | empty |
| 3 | 471 | 0.64 | 0.77 | 46 | empty |
| 4 | 278 | 0.63 | 0.81 | 37 | empty |
| 5 | 89 | 0.53 | 0.85 | 20 | empty |
Interfaces
9 interfaces between chains.
- A–B · 1402 Ų buried · 19 hydrogen bonds · protein-protein
- E–F · 1393 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 957 Ų buried · 20 hydrogen bonds · protein-protein
- E–G · 952 Ų buried · 22 hydrogen bonds · protein-protein
- A–D · 728 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 1IM9 · Crystal structure of the human natural killer cell inhibitory receptor KIR2DL1 bound to… · the same entry in another collection · chain G against G, TM-score 1.00
- P43626 · AlphaFold monomer V2.0 prediction for killer cell immunoglobulin-like receptor 2DL1… · a predicted model of the same protein · chain D against A, TM-score 0.97
- P61769 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P61769) · a predicted model of the same protein · chain B against A, TM-score 0.97
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
- Every structure of UniProt P43626
- Elsewhere: RCSB PDB 1IM9 · PDBe 1IM9 · UniProt P30504 · UniProt P61769 · UniProt P43626
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