Research workbench
RXR LBD in complex with 9-cis-13,14-dihydroretinoic acid
Analyse RXR LBD in complex with 9-cis-13,14-dihydroretinoic acid in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ZSH
- Type
- protein
- Length
- 224 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.8
- Source
- Homo sapiens; SYNTHETIC CONSTRUCT
- Molecule
- Retinoic acid receptor RXR-alpha; NCoA2 peptide
- UniProt
- P19793
- Ligands
- 4XW
- Pockets
- 2 · best druggability 0.84
Structure
x-ray diffraction · resolution 1.8 · 2 distinct chains · 69% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Retinoic acid receptor RXR-alpha | protein | 213 | 69% helix, 3% strand | P19793 |
| B | NCoA2 peptide | protein | 11 | 64% helix, 0% strand | — |
Ligands and binding sites
- 4XW · (5S,6S,9R,13R)-2,3-didehydro-5,6,7,8,9,10,11,12,13,14-decahydroretinoic acid · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 311 | 0.84 | 0.94 | 43 | 4XW |
| 2 | 162 | 0.43 | 0.74 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 578 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 4ZSH · Rxr lbd in complex with 9-cis-13,14-dihydroretinoic acid · the same entry in another collection · chain A against A, TM-score 1.00
- P19793 · AlphaFold monomer V2.0 prediction for retinoic acid receptor rxr- alpha (P19793) · 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 P19793
- Elsewhere: RCSB PDB 4ZSH · PDBe 4ZSH · UniProt P19793
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