MolNFT v1 · #155550 · protein
Crystal structure of dimeric rxr-lbd complexed with full agonist net- 3IB and TIF2 co-activator
6LB5 · Retinoic acid receptor rxr-alpha: “Crystal structure of dimeric rxr-lbd complexed with full agonist net- 3IB and TIF2 co-activator”. X-ray diffraction, 1 ligand (E80), 4 pockets (best druggability 0.85). MolNFT v1 #155550 on…
- PDB
- 6LB5
- Type
- protein
- Length
- 452 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Retinoic acid receptor rxr-alpha; Nuclear receptor coactivator 2
- UniProt
- P19793, Q15596
- Ligands
- E80
- Pockets
- 4 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 69% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Retinoic acid receptor rxr-alpha | protein | 211 | 68% helix, 3% strand | P19793 |
| B | Nuclear receptor coactivator 2 | protein | 10 | 70% helix, 0% strand | Q15596 |
| C | Retinoic acid receptor rxr-alpha | protein | 220 | 70% helix, 2% strand | P19793 |
| D | Nuclear receptor coactivator 2 | protein | 11 | 73% helix, 0% strand | Q15596 |
Ligands and binding sites
- E80 · 6-[ethyl-[3-(2-methylpropoxy)-4-propan-2-yl-phenyl]amino]pyridine-3-carboxylic acid · ligand · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 339 | 0.85 | 0.94 | 47 | E80 |
| 2 | 295 | 0.84 | 0.94 | 44 | E80 |
| 3 | 593 | 0.67 | 0.77 | 52 | empty |
| 4 | 75 | 0.52 | 0.85 | 20 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1150 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 582 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 559 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 6LB5 · Crystal structure of dimeric RXR-LBD complexed with full agonist NEt-3IB and TIF2… · 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 6LB5 · PDBe 6LB5 · UniProt P19793 · UniProt Q15596
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