Research workbench
Crystal structure of platynereis dumerilii rar ligand-binding domain in complex with all-trans retinoic acid
Analyse Crystal structure of platynereis dumerilii rar ligand-binding domain in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6EU9
- Type
- protein
- Length
- 898 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Retinoic acid receptor
- Ligands
- REA
- Pockets
- 16 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 67% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Retinoic acid receptor | protein | 227 | 68% helix, 4% strand | — |
| C | Retinoic acid receptor | protein | 217 | 65% helix, 4% strand | — |
Ligands and binding sites
- REA · Retinoic acid · ligand · 2 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 864 | 0.82 | 0.84 | 103 | empty |
| 2 | 507 | 0.79 | 0.85 | 58 | empty |
| 3 | 816 | 0.77 | 0.81 | 86 | REA |
| 4 | 882 | 0.76 | 0.79 | 90 | REA |
| 5 | 98 | 0.61 | 0.88 | 26 | empty |
Interfaces
3 interfaces between chains.
- A–D · 1267 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 1214 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 267 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 6EU9 · Crystal structure of Platynereis dumerilii RAR ligand-binding domain in complex with… · 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
- Elsewhere: RCSB PDB 6EU9 · PDBe 6EU9
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.