Research workbench
Crystal structure of rarb lbd in complex with 9CIS retinoic acid
Analyse Crystal structure of rarb lbd in complex with 9CIS retinoic acid in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4DM8
- Type
- protein
- Length
- 493 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Retinoic acid receptor beta; Nuclear receptor coactivator 1
- EC
- 2.3.1.48
- UniProt
- P10826, Q15788
- Ligands
- REA
- Pockets
- 10 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 66% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Retinoic acid receptor beta | protein | 238 | 66% helix, 4% strand | P10826 |
| B | Retinoic acid receptor beta | protein | 239 | 66% helix, 4% strand | P10826 |
| C, D | Nuclear receptor coactivator 1 (EC 2.3.1.48) | protein | 8 | 75% helix, 0% strand | Q15788 |
Ligands and binding sites
- REA · Retinoic acid · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 223 | 0.84 | 0.96 | 33 | REA |
| 2 | 199 | 0.83 | 0.96 | 29 | REA |
| 3 | 414 | 0.68 | 0.80 | 31 | empty |
| 4 | 330 | 0.62 | 0.79 | 26 | empty |
| 5 | 83 | 0.50 | 0.83 | 20 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1165 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 483 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 480 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 4DM8 · Crystal structure of RARb LBD in complex with 9cis retinoic acid · the same entry in another collection · chain B against B, TM-score 1.00
- P10826 · AlphaFold monomer V2.0 prediction for retinoic acid receptor beta (P10826) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P10826
- Every structure of UniProt Q15788
- Elsewhere: RCSB PDB 4DM8 · PDBe 4DM8 · UniProt P10826 · UniProt Q15788
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