Research workbench
NKG2D in complex with ULBP3
Analyse NKG2D in complex with ULBP3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1KCG
- Type
- protein
- Length
- 415 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NKG2-D type II integral membrane protein; ULBP3 protein
- UniProt
- P26718, Q9BZM4
- Ligands
- GSH
- Pockets
- 6 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 22% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NKG2-D type II integral membrane protein | protein | 122 | 11% helix, 43% strand | P26718 |
| B | NKG2-D type II integral membrane protein | protein | 123 | 11% helix, 42% strand | P26718 |
| C | ULBP3 protein | protein | 170 | 38% helix, 31% strand | Q9BZM4 |
Ligands and binding sites
- GSH · Glutathione · ligand · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 53 | 0.71 | 0.97 | 12 | empty |
| 2 | 374 | 0.67 | 0.81 | 62 | empty |
| 3 | 318 | 0.60 | 0.78 | 34 | empty |
| 4 | 80 | 0.33 | 0.74 | 16 | empty |
| 5 | 54 | 0.31 | 0.77 | 14 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1045 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 553 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 508 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 1 covalent (disulfide, covalent ligand).
Compared structures
- 1KCG · NKG2D in complex with ULBP3 · the same entry in another collection · chain A against A, TM-score 1.00
- P26718 · AlphaFold monomer V2.0 prediction for NKG2-D type II integral membrane protein (P26718) · a predicted model of the same protein · chain B against A, TM-score 0.98
- Q9BZM4 · AlphaFold monomer V2.0 prediction for UL16-binding protein 3 (Q9BZM4) · a predicted model of the same protein · chain C against A, TM-score 0.96
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 P26718
- Every structure of UniProt Q9BZM4
- Elsewhere: RCSB PDB 1KCG · PDBe 1KCG · UniProt P26718 · UniProt Q9BZM4
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.