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Crystal structure of a complex between B7-H6, a tumor cell ligand for natural cytotoxicity receptor NKP30, and an inhibitory antibody
Analyse Crystal structure of a complex between B7-H6, a tumor cell ligand for natural… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ZSO
- Type
- protein
- Length
- 1,296 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antibody light chain; Antibody heavy chain; Natural cytotoxicity triggering receptor 3…
- UniProt
- Q68D85
- Ligands
- NAG, FUC, SO4
- Pockets
- 16 · best druggability 0.68
Structure
x-ray diffraction · 5 distinct chains · 8% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Antibody light chain | protein | 214 | 6% helix, 51% strand | — |
| B | Antibody heavy chain | protein | 218 | 11% helix, 55% strand | — |
| D | Antibody heavy chain | protein | 219 | 11% helix, 53% strand | — |
| E | Natural cytotoxicity triggering receptor 3 ligand 1 | protein | 217 | 6% helix, 51% strand | Q68D85 |
| F | Natural cytotoxicity triggering receptor 3 ligand 1 | protein | 214 | 5% helix, 50% strand | Q68D85 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains E, F
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains B, E, D, F
- SO4 · Sulfate ion · ion · 2 copies · chains B, D
- ACY · Acetic acid · additive · 2 copies · chains A, B, E, C, D, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 846 | 0.68 | 0.75 | 83 | empty |
| 2 | 438 | 0.58 | 0.75 | 53 | empty |
| 3 | 73 | 0.54 | 0.86 | 16 | ACY |
| 4 | 73 | 0.53 | 0.85 | 12 | ACY |
| 5 | 339 | 0.52 | 0.73 | 44 | empty |
Interfaces
8 interfaces between chains.
- A–B · 1934 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 1908 Ų buried · 16 hydrogen bonds · protein-protein
- D–F · 641 Ų buried · 6 hydrogen bonds · protein-protein
- B–E · 630 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 306 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 4ZSO · Crystal structure of a complex between B7-H6, a tumor cell ligand for natural… · the same entry in another collection · chain F against F, 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 0.98
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 Q68D85
- Elsewhere: RCSB PDB 4ZSO · PDBe 4ZSO · UniProt Q68D85
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