MolNFT v1 · #69316 · protein
Crystal structure of raralpha ligand binding domain in complex with an agonist ligand (AM580) and a coactivator fragment
3KMR · Retinoic acid receptor alpha: “Crystal structure of raralpha ligand binding domain in complex with an agonist ligand (AM580) and a…”. X-ray diffraction, 1 ligand (EQN), 3 pockets (best druggability 0.81). MolNFT v1 #69316 on…
- PDB
- 3KMR
- Type
- protein
- Length
- 244 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Retinoic acid receptor alpha; Nuclear receptor coactivator 1
- EC
- 2.3.1.48
- UniProt
- P10276, Q15788
- Ligands
- EQN
- Pockets
- 3 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 69% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Retinoic acid receptor alpha | protein | 234 | 69% helix, 4% strand | P10276 |
| C | Nuclear receptor coactivator 1 (EC 2.3.1.48) | protein | 10 | 80% helix, 0% strand | Q15788 |
Ligands and binding sites
- EQN · 4-{[(5,5,8,8-tetramethyl-5,6,7,8-tetrahydronaphthalen-2-yl)carbonyl]amino}benzoic acid · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 185 | 0.81 | 0.95 | 33 | EQN |
| 2 | 105 | 0.44 | 0.78 | 17 | empty |
| 3 | 80 | 0.34 | 0.75 | 17 | empty |
Interfaces
1 interface between chains.
- A–C · 507 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 3KMR · Crystal structure of RARalpha ligand binding domain in complex with an agonist ligand… · 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 Q15788
- Elsewhere: RCSB PDB 3KMR · PDBe 3KMR · UniProt P10276 · UniProt Q15788
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.