Research workbench
Killer cell immunoglobulin-like receptor 2DL2 in complex with HLA- C*07:02
Analyse Killer cell immunoglobulin-like receptor 2DL2 in complex with HLA- C*07:02 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6PA1
- Type
- protein
- Length
- 1,131 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HLA class I histocompatibility antigen, cw-7 alpha chain; Beta-2-microglobulin…
- UniProt
- P10321, P61769, P43627
- Pockets
- 16 · best druggability 0.74
Structure
x-ray diffraction · 7 distinct chains · 12% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HLA class I histocompatibility antigen, cw-7 alpha chain | protein | 271 | 23% helix, 39% strand | P10321 |
| B | Beta-2-microglobulin | protein | 99 | 0% helix, 49% strand | P61769 |
| C, G | Arg-tyr-arg-pro-gly-thr-val-ala-leu | protein | 9 | 0% helix, 0% strand | — |
| D | Killer cell immunoglobulin-like receptor 2DL2 | protein | 188 | 2% helix, 51% strand | P43627 |
| E | HLA class I histocompatibility antigen, cw-7 alpha chain | protein | 269 | 23% helix, 40% strand | P10321 |
| F | Beta-2-microglobulin | protein | 100 | 0% helix, 51% strand | P61769 |
| H | Killer cell immunoglobulin-like receptor 2DL2 | protein | 186 | 2% helix, 50% strand | P43627 |
Pockets
16 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 988 | 0.74 | 0.77 | 101 | empty |
| 2 | 604 | 0.67 | 0.76 | 54 | empty |
| 3 | 552 | 0.65 | 0.76 | 46 | empty |
| 4 | 359 | 0.59 | 0.77 | 40 | empty |
| 5 | 146 | 0.52 | 0.80 | 25 | empty |
Interfaces
15 interfaces between chains.
- A–B · 1275 Ų buried · 14 hydrogen bonds · protein-protein
- E–F · 1273 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 980 Ų buried · 13 hydrogen bonds · protein-protein
- E–G · 975 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 855 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 6PA1 · Killer cell immunoglobulin-like receptor 2DL2 in complex with HLA-C*07:02 · the same entry in another collection · chain H against H, 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 0.97
- P43627 · AlphaFold monomer V2.0 prediction for killer cell immunoglobulin-like receptor 2DL2… · a predicted model of the same protein · chain H against A, TM-score 0.94
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 P10321
- Every structure of UniProt P61769
- Every structure of UniProt P43627
- Elsewhere: RCSB PDB 6PA1 · PDBe 6PA1 · UniProt P10321 · UniProt P61769 · UniProt P43627
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