Research workbench
Crystal structure of a complex between glycosylated NKP30 and its deglycosylated tumour ligand B7-H6
Analyse Crystal structure of a complex between glycosylated NKP30 and its… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6YJP
- Type
- protein
- Length
- 875 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Natural cytotoxicity triggering receptor 3 ligand 1; Natural cytotoxicity triggering…
- UniProt
- Q68D85, O14931
- Ligands
- NAG
- Pockets
- 9 · best druggability 0.66
Structure
x-ray diffraction · 4 distinct chains · 5% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Natural cytotoxicity triggering receptor 3 ligand 1 | protein | 225 | 4% helix, 48% strand | Q68D85 |
| D | Natural cytotoxicity triggering receptor 3 ligand 1 | protein | 214 | 5% helix, 51% strand | Q68D85 |
| A, B | Natural cytotoxicity triggering receptor 3 | protein | 111 | 9% helix, 39% strand | O14931 |
| E | Natural cytotoxicity triggering receptor 3 ligand 1 | protein | 214 | 5% helix, 53% strand | Q68D85 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains C, E, D, A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 504 | 0.66 | 0.77 | 51 | empty |
| 2 | 398 | 0.65 | 0.79 | 47 | empty |
| 3 | 367 | 0.63 | 0.78 | 40 | empty |
| 4 | 353 | 0.62 | 0.78 | 36 | empty |
| 5 | 143 | 0.50 | 0.79 | 33 | empty |
Interfaces
5 interfaces between chains.
- C–D · 883 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 845 Ų buried · 5 hydrogen bonds · protein-protein
- C–A · 592 Ų buried · 4 hydrogen bonds · protein-protein
- C–E · 528 Ų buried · 7 hydrogen bonds · protein-protein
- D–E · 308 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 5 glycan (disulfide, N-glycosylation).
Compared structures
- 6YJP · Crystal structure of a complex between glycosylated NKp30 and its deglycosylated tumour… · the same entry in another collection · chain E against E, TM-score 1.00
- Q68D85 · AlphaFold monomer V2.0 prediction for natural cytotoxicity triggering receptor 3 ligand 1… · a predicted model of the same protein · chain E against A, TM-score 0.97
- O14931 · AlphaFold monomer V2.0 prediction for natural cytotoxicity triggering receptor 3 (O14931) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 Q68D85
- Every structure of UniProt O14931
- Elsewhere: RCSB PDB 6YJP · PDBe 6YJP · UniProt Q68D85 · UniProt O14931
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