MolNFT v1 · #92359 · protein
Crystal structure of the murine cytomegalovirus MHC-I homolog M152 with ligand rae-1 gamma
4G59 · Retinoic acid early-inducible protein 1-gamma: “Crystal structure of the murine cytomegalovirus MHC-I homolog M152 with ligand rae-1 gamma”. X-ray diffraction, 1 ligand (NAG), 7 pockets (best druggability 0.82). MolNFT v1 #92359 on…
- PDB
- 4G59
- Type
- protein
- Length
- 853 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Retinoic acid early-inducible protein 1-gamma; M152 protein
- UniProt
- O08604, Q83156
- Ligands
- NAG
- Pockets
- 7 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 30% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Retinoic acid early-inducible protein 1-gamma | protein | 162 | 35% helix, 28% strand | O08604 |
| C, D | M152 protein | protein | 264 | 22% helix, 39% strand | Q83156 |
| B | Retinoic acid early-inducible protein 1-gamma | protein | 163 | 37% helix, 27% strand | O08604 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1025 | 0.82 | 0.84 | 113 | empty |
| 2 | 383 | 0.63 | 0.78 | 51 | empty |
| 3 | 349 | 0.56 | 0.75 | 37 | empty |
| 4 | 52 | 0.46 | 0.85 | 18 | empty |
| 5 | 69 | 0.39 | 0.78 | 15 | empty |
Interfaces
4 interfaces between chains.
- A–C · 1436 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 1364 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 711 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 116 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 4G59 · Crystal structure of the murine cytomegalovirus MHC-I homolog m152 with ligand RAE-1 gamma · the same entry in another collection · chain A against A, TM-score 1.00
- O08604 · AlphaFold monomer V2.0 prediction for retinoic acid early-inducible protein 1-gamma… · a predicted model of the same protein · chain A 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 O08604
- Every structure of UniProt Q83156
- Elsewhere: RCSB PDB 4G59 · PDBe 4G59 · UniProt O08604 · UniProt Q83156
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.