Research workbench
Crystal structure of human retinoic X receptor alpha complexed with bigelovin and coactivator src-1
Analyse Crystal structure of human retinoic X receptor alpha complexed with bigelovin… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3OZJ
- Type
- protein
- Length
- 451 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Retinoic acid receptor rxr-alpha; Src-1, peptide of nuclear receptor coactivator 2
- UniProt
- P19793, Q15596
- Ligands
- BGV
- Pockets
- 5 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 65% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Retinoic acid receptor rxr-alpha | protein | 215 | 66% helix, 3% strand | P19793 |
| B | Src-1, peptide of nuclear receptor coactivator 2 | protein | 10 | 80% helix, 0% strand | Q15596 |
| D | Src-1, peptide of nuclear receptor coactivator 2 | protein | 11 | 45% helix, 0% strand | Q15596 |
Ligands and binding sites
- BGV · (3aR,4S,4aR,7aR,8R,9aS)-4a,8-dimethyl-3-methylidene-2,5-dioxo-2,3,3a,4,4a,5,7a,8,9,9a-decahydroazuleno[6,5-b]furan-4-yl acetate · ligand · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 267 | 0.84 | 0.95 | 31 | BGV |
| 2 | 356 | 0.84 | 0.92 | 43 | BGV |
| 3 | 815 | 0.71 | 0.77 | 58 | empty |
| 4 | 67 | 0.58 | 0.89 | 15 | empty |
| 5 | 105 | 0.55 | 0.84 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1182 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 550 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 547 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 3OZJ · Crystal structure of human retinoic X receptor alpha complexed with bigelovin and… · the same entry in another collection · chain A against A, TM-score 1.00
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 P19793
- Every structure of UniProt Q15596
- Elsewhere: RCSB PDB 3OZJ · PDBe 3OZJ · UniProt P19793 · UniProt Q15596
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