MolNFT v1 · #101407 · protein + DNA
Crystal structure of liganded hrxr-ALPHA/HLXR-beta heterodimer on DNA
4NQA · Retinoic acid receptor rxr-alpha: “Crystal structure of liganded hrxr-ALPHA/HLXR-beta heterodimer on DNA”. X-ray diffraction, 3 ligands (9CR, 965, ZN), 20 pockets (best druggability 0.86). MolNFT v1 #101407 on GenesisL1: 3D…
- PDB
- 4NQA
- Type
- protein + DNA
- Length
- 1,507 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Retinoic acid receptor rxr-alpha; Liver X nuclear receptor beta; Nuclear receptor…
- UniProt
- P19793, F1D8P7, Q15596
- Ligands
- 9CR, 965, ZN
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 9 distinct chains · 53% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Retinoic acid receptor rxr-alpha | protein | 317 | 56% helix, 2% strand | P19793 |
| B | Liver X nuclear receptor beta | protein | 369 | 53% helix, 4% strand | F1D8P7 |
| C | Nuclear receptor coactivator 2 | protein | 10 | 70% helix, 0% strand | Q15596 |
| D, J | Nuclear receptor coactivator 2 | protein | 12 | 58% helix, 0% strand | Q15596 |
| E, L | 5'-D(*TP*AP*AP*GP*GP*TP*CP*AP*CP*TP*TP*CP*AP*GP*GP*TP*CP*A) -3' | dna | 18 | — | — |
| F, M | 5'-D(*TP*AP*TP*GP*AP*CP*CP*TP*GP*AP*AP*GP*TP*GP*AP*CP*CP*T) -3' | dna | 18 | — | — |
| H | Retinoic acid receptor rxr-alpha | protein | 319 | 54% helix, 3% strand | P19793 |
| I | Liver X nuclear receptor beta | protein | 385 | 48% helix, 3% strand | F1D8P7 |
| K | Nuclear receptor coactivator 2 | protein | 11 | 73% helix, 0% strand | Q15596 |
Ligands and binding sites
- 9CR · (9cis)-retinoic acid · ligand · 2 copies · chains A, H
- 965 · [3-(3-{[2-chloro-3-(trifluoromethyl)benzyl](2,2-diphenylethyl)amino}propoxy)phenyl]acetic acid · ligand · 2 copies · chains B, I
- ZN · Zinc ion · metal · 8 copies · chains A, B, H, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 373 | 0.86 | 0.95 | 45 | 965 |
| 2 | 267 | 0.85 | 0.96 | 41 | 9CR |
| 3 | 236 | 0.84 | 0.96 | 27 | 9CR |
| 4 | 509 | 0.82 | 0.88 | 56 | 965 |
| 5 | 738 | 0.75 | 0.80 | 60 | empty |
Interfaces
18 interfaces between chains.
- H–I · 2129 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1870 Ų buried · 14 hydrogen bonds · protein-protein
- B–F · 815 Ų buried · 17 hydrogen bonds · protein-nucleic
- L–M · 765 Ų buried · 79 hydrogen bonds · nucleic-nucleic
- E–F · 764 Ų buried · 86 hydrogen bonds · nucleic-nucleic
Compared structures
- 4NQA · Crystal structure of liganded hRXR-alpha/hLXR-beta heterodimer on DNA · 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 F1D8P7
- Every structure of UniProt Q15596
- Elsewhere: RCSB PDB 4NQA · PDBe 4NQA · UniProt P19793 · UniProt F1D8P7 · UniProt Q15596
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