MolNFT v1 · #106490 · protein
Crystal structure of NKG2D in complex with ULBP6
4S0U · NKG2-D type II integral membrane protein: “Crystal structure of NKG2D in complex with ULBP6”. X-ray diffraction, 3 pockets (best druggability 0.80). MolNFT v1 #106490 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4S0U
- Type
- protein
- Length
- 425 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NKG2-D type II integral membrane protein; Retinoic acid early transcript 1L protein
- UniProt
- P26718, Q5VY80
- Pockets
- 3 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 23% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NKG2-D type II integral membrane protein | protein | 124 | 12% helix, 44% strand | P26718 |
| B | NKG2-D type II integral membrane protein | protein | 126 | 11% helix, 44% strand | P26718 |
| C | Retinoic acid early transcript 1L protein | protein | 175 | 39% helix, 31% strand | Q5VY80 |
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 103 | 0.80 | 0.98 | 17 | empty |
| 2 | 474 | 0.63 | 0.76 | 51 | empty |
| 3 | 220 | 0.52 | 0.77 | 36 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1163 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 621 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 544 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 4S0U · Crystal structure of NKG2D in complex with ULBP6 · 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 A against A, TM-score 0.97
- Q5VY80 · AlphaFold monomer V2.0 prediction for UL16-binding protein 6 (Q5VY80) · 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 Q5VY80
- Elsewhere: RCSB PDB 4S0U · PDBe 4S0U · UniProt P26718 · UniProt Q5VY80
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