MolNFT v1 · #175080 · protein
Crystal structure of human rxralpha ligand binding domain complexed with cbtf-ee.
7CFO · Retinoic acid receptor rxr-alpha: “Crystal structure of human rxralpha ligand binding domain complexed with cbtf-ee.”. X-ray diffraction, 1 ligand (WZ6), 7 pockets (best druggability 0.84). MolNFT v1 #175080 on GenesisL1: 3D…
- PDB
- 7CFO
- Type
- protein
- Length
- 792 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Retinoic acid receptor rxr-alpha
- UniProt
- P19793
- Ligands
- WZ6
- Pockets
- 7 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 74% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Retinoic acid receptor rxr-alpha | protein | 193 | 73% helix, 3% strand | P19793 |
| B | Retinoic acid receptor rxr-alpha | protein | 206 | 74% helix, 2% strand | P19793 |
| C | Retinoic acid receptor rxr-alpha | protein | 206 | 74% helix, 2% strand | P19793 |
| D | Retinoic acid receptor rxr-alpha | protein | 187 | 74% helix, 2% strand | P19793 |
Ligands and binding sites
- WZ6 · 1-[3-(2-ethoxyethoxy)-5,5,8,8-tetramethyl-6,7-dihydronaphthalen-2-yl]-2-(trifluoromethyl) benzimidazole-5-carboxylic acid · ligand · 3 copies · chains A, C, B, D
- GOL · Glycerol · additive · 2 copies · chains A, B, 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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 702 | 0.84 | 0.87 | 59 | WZ6 |
| 2 | 858 | 0.82 | 0.84 | 85 | WZ6 |
| 3 | 176 | 0.67 | 0.87 | 20 | empty |
| 4 | 266 | 0.66 | 0.82 | 33 | empty |
| 5 | 122 | 0.59 | 0.86 | 21 | GOL |
Interfaces
5 interfaces between chains.
- A–C · 1405 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 1380 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1284 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 1222 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 16 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 7CFO · Crystal structure of human RXRalpha ligand binding domain complexed with CBTF-EE. · 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
- Elsewhere: RCSB PDB 7CFO · PDBe 7CFO · UniProt P19793
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