MolNFT v1 · #173123 · protein
Crystal structure of raralpha ligand binding domain in complex with a fragment of the TIF2 coactivator
7APO · Retinoic acid receptor alpha: “Crystal structure of raralpha ligand binding domain in complex with a fragment of the TIF2 coactivator”. X-ray diffraction, 1 ligand (EQN), 9 pockets (best druggability 0.80). MolNFT v1 #173123 on…
- PDB
- 7APO
- Type
- protein
- Length
- 518 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Retinoic acid receptor alpha; Nuclear receptor coactivator 2
- UniProt
- P10276, E7EWM1
- Ligands
- EQN
- Pockets
- 9 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 68% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Retinoic acid receptor alpha | protein | 233 | 67% helix, 4% strand | P10276 |
| B | Retinoic acid receptor alpha | protein | 233 | 70% helix, 4% strand | P10276 |
| C, D | Nuclear receptor coactivator 2 | protein | 26 | 73% helix, 0% strand | E7EWM1 |
Ligands and binding sites
- EQN · 4-{[(5,5,8,8-tetramethyl-5,6,7,8-tetrahydronaphthalen-2-yl)carbonyl]amino}benzoic acid · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 234 | 0.80 | 0.92 | 38 | EQN |
| 2 | 252 | 0.80 | 0.92 | 38 | EQN |
| 3 | 429 | 0.67 | 0.79 | 39 | empty |
| 4 | 428 | 0.66 | 0.78 | 37 | empty |
| 5 | 144 | 0.50 | 0.79 | 22 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1347 Ų buried · 15 hydrogen bonds · protein-protein
- B–D · 679 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 677 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 7APO · Crystal structure of RARalpha ligand binding domain in complex with a fragment of the… · 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 A against A, TM-score 0.99
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 P10276
- Every structure of UniProt E7EWM1
- Elsewhere: RCSB PDB 7APO · PDBe 7APO · UniProt P10276 · UniProt E7EWM1
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