Research workbench
Crystal structure of multi-domain rar-beta-rxr-alpha heterodimer on DNA
Analyse Crystal structure of multi-domain rar-beta-rxr-alpha heterodimer on DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5UAN
- Type
- protein + DNA
- Length
- 639 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Retinoic acid receptor rxr-alpha; Retinoic acid receptor beta; Nuclear receptor…
- UniProt
- P19793, P10826, E7EWM1
- Ligands
- 9CR, REA, ZN
- Pockets
- 11 · best druggability 0.84
Structure
x-ray diffraction · 6 distinct chains · 59% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Retinoic acid receptor rxr-alpha | protein | 278 | 61% helix, 5% strand | P19793 |
| B | Retinoic acid receptor beta | protein | 308 | 57% helix, 5% strand | P10826 |
| C | Nuclear receptor coactivator 2 | protein | 10 | 50% helix, 0% strand | E7EWM1 |
| D | Nuclear receptor coactivator 2 | protein | 9 | 78% helix, 0% strand | E7EWM1 |
| E | DNA (5'- D(*CP*TP*AP*GP*GP*TP*CP*AP*AP*AP*GP*GP*TP*CP*AP*GP*C)-3') | dna | 17 | — | — |
| F | DNA (5'- D(*GP*CP*TP*GP*AP*CP*CP*TP*TP*TP*GP*AP*CP*CP*TP*AP*G)-3') | dna | 17 | — | — |
Ligands and binding sites
- 9CR · (9cis)-retinoic acid · ligand · chains A
- REA · Retinoic acid · ligand · chains B
- ZN · Zinc ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 203 | 0.84 | 0.97 | 31 | REA |
| 2 | 238 | 0.83 | 0.95 | 32 | 9CR |
| 3 | 562 | 0.64 | 0.76 | 39 | empty |
| 4 | 545 | 0.64 | 0.76 | 55 | empty |
| 5 | 405 | 0.63 | 0.78 | 29 | empty |
Interfaces
8 interfaces between chains.
- A–B · 1219 Ų buried · 16 hydrogen bonds · protein-protein
- E–F · 760 Ų buried · 58 hydrogen bonds · nucleic-nucleic
- A–E · 494 Ų buried · 13 hydrogen bonds · protein-nucleic
- B–D · 492 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 451 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5UAN · Crystal structure of multi-domain RAR-beta-RXR-alpha heterodimer on DNA · the same entry in another collection · chain C against C, TM-score 1.00
- P10826 · AlphaFold monomer V2.0 prediction for retinoic acid receptor beta (P10826) · a predicted model of the same protein · chain B 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 P10826
- Every structure of UniProt E7EWM1
- Elsewhere: RCSB PDB 5UAN · PDBe 5UAN · UniProt P19793 · UniProt P10826 · UniProt E7EWM1
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