MolNFT v1 · #38054 · protein
Human retinoic acid receptor rxr-gamma ligand-binding domain
2GL8: “Human retinoic acid receptor rxr-gamma ligand-binding domain”. X-ray diffraction, 12 pockets (best druggability 0.70). MolNFT v1 #38054 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2GL8
- Type
- protein
- Length
- 771 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Retinoic acid receptor rxr-gamma
- UniProt
- P48443
- Pockets
- 12 · best druggability 0.70
Structure
x-ray diffraction · 4 distinct chains · 61% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Retinoic acid receptor rxr-gamma | protein | 190 | 63% helix, 4% strand | P48443 |
| B | Retinoic acid receptor rxr-gamma | protein | 192 | 63% helix, 2% strand | P48443 |
| C | Retinoic acid receptor rxr-gamma | protein | 194 | 58% helix, 2% strand | P48443 |
| D | Retinoic acid receptor rxr-gamma | protein | 195 | 61% helix, 2% strand | P48443 |
Pockets
12 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 584 | 0.70 | 0.79 | 60 | empty |
| 2 | 346 | 0.65 | 0.80 | 45 | empty |
| 3 | 348 | 0.65 | 0.79 | 36 | empty |
| 4 | 309 | 0.61 | 0.79 | 29 | empty |
| 5 | 208 | 0.59 | 0.80 | 25 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1113 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 1108 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 505 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 420 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2GL8 · Human Retinoic acid receptor RXR-gamma ligand-binding domain · the same entry in another collection · chain D against D, TM-score 1.00
- P48443 · AlphaFold monomer V2.0 prediction for retinoic acid receptor rxr- gamma (P48443) · a predicted model of the same protein · chain A against A, TM-score 0.93
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 P48443
- Elsewhere: RCSB PDB 2GL8 · PDBe 2GL8 · UniProt P48443
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