Research workbench
Crystal structure of the RARALPHA/RXRALPHA ligand binding domain heterodimer in complex with a fragment of SRC1 coactivator
Analyse Crystal structure of the RARALPHA/RXRALPHA ligand binding domain heterodimer in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7AOS
- Type
- protein
- Length
- 475 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Retinoic acid receptor rxr-alpha; Retinoic acid receptor alpha; Nuclear receptor…
- EC
- 2.3.1.48
- UniProt
- P28700, P10276, Q15788
- Ligands
- LG2, EQN
- Pockets
- 8 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 66% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Retinoic acid receptor rxr-alpha | protein | 216 | 66% helix, 3% strand | P28700 |
| B | Retinoic acid receptor alpha | protein | 241 | 66% helix, 4% strand | P10276 |
| C | Nuclear receptor coactivator 1 (EC 2.3.1.48) | protein | 11 | 73% helix, 0% strand | Q15788 |
| D | Nuclear receptor coactivator 1 (EC 2.3.1.48) | protein | 7 | 57% helix, 0% strand | Q15788 |
Ligands and binding sites
- LG2 · 6-[1-(3,5,5,8,8-pentamethyl-5,6,7,8-tetrahydronaphthalen-2-yl)cyclopropyl]pyridine-3-carboxylic acid · ligand · chains A
- EQN · 4-{[(5,5,8,8-tetramethyl-5,6,7,8-tetrahydronaphthalen-2-yl)carbonyl]amino}benzoic acid · ligand · chains B
- GOL · Glycerol · additive
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 220 | 0.84 | 0.96 | 27 | LG2 |
| 2 | 198 | 0.80 | 0.94 | 35 | EQN |
| 3 | 571 | 0.66 | 0.76 | 56 | empty |
| 4 | 95 | 0.53 | 0.84 | 17 | empty |
| 5 | 144 | 0.49 | 0.78 | 24 | empty |
Interfaces
3 interfaces between chains.
- A–B · 995 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 527 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 416 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 7AOS · crystal structure of the RARalpha/RXRalpha ligand binding domain heterodimer in complex… · the same entry in another collection · chain A against A, TM-score 1.00
- P10276 · AlphaFold monomer V2.0 prediction for retinoic acid receptor alpha (P10276) · a predicted model of the same protein · chain B against A, TM-score 0.98
- P28700 · AlphaFold monomer V2.0 prediction for retinoic acid receptor rxr- alpha (P28700) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 P28700
- Every structure of UniProt P10276
- Every structure of UniProt Q15788
- Elsewhere: RCSB PDB 7AOS · PDBe 7AOS · UniProt P28700 · UniProt P10276 · UniProt Q15788
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