Research workbench
Crystal structure of murine nk cell ligand rae-1 beta in complex with NKG2D
Analyse Crystal structure of murine nk cell ligand rae-1 beta in complex with NKG2D in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4PP8
- Type
- protein
- Length
- 546 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NKG2-D type II integral membrane protein; Retinoic acid early-inducible protein 1-beta
- UniProt
- O54709, O08603
- Pockets
- 7 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 31% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | NKG2-D type II integral membrane protein | protein | 125 | 12% helix, 41% strand | O54709 |
| C | Retinoic acid early-inducible protein 1-beta | protein | 146 | 39% helix, 30% strand | O08603 |
| D | Retinoic acid early-inducible protein 1-beta | protein | 150 | 39% helix, 31% strand | O08603 |
Ligands and binding sites
- GOL · Glycerol · additive · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 106 | 0.73 | 0.95 | 26 | empty |
| 2 | 328 | 0.57 | 0.76 | 49 | empty |
| 3 | 165 | 0.44 | 0.75 | 26 | GOL |
| 4 | 135 | 0.44 | 0.76 | 21 | empty |
| 5 | 55 | 0.36 | 0.79 | 15 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1221 Ų buried · 23 hydrogen bonds · protein-protein
- B–C · 516 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 459 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 208 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 4PP8 · Crystal structure of murine NK cell ligand RAE-1 beta in complex with NKG2D · the same entry in another collection · chain A against A, TM-score 1.00
- O08603 · AlphaFold monomer V2.0 prediction for retinoic acid early-inducible protein 1-beta… · a predicted model of the same protein · chain C against A, TM-score 0.99
- O54709 · AlphaFold monomer V2.0 prediction for NKG2-D type II integral membrane protein (O54709) · 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 O54709
- Every structure of UniProt O08603
- Elsewhere: RCSB PDB 4PP8 · PDBe 4PP8 · UniProt O54709 · UniProt O08603
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