Research workbench
Rxra structure complexed with cu-6PMN
Analyse Rxra structure complexed with cu-6PMN in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6JNO
- Type
- protein
- Length
- 791 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Retinoic acid receptor rxr-alpha
- UniProt
- P19793
- Ligands
- WY5
- Pockets
- 6 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 74% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Retinoic acid receptor rxr-alpha | protein | 195 | 75% helix, 3% strand | P19793 |
| B | Retinoic acid receptor rxr-alpha | protein | 193 | 75% helix, 3% strand | P19793 |
| C | Retinoic acid receptor rxr-alpha | protein | 200 | 75% helix, 2% strand | P19793 |
| D | Retinoic acid receptor rxr-alpha | protein | 203 | 73% helix, 3% strand | P19793 |
Ligands and binding sites
- WY5 · 7-oxidanyl-2-oxidanylidene-6-(3,5,5,8,8-pentamethyl-6, 7-dihydronaphthalen-2-yl)chromene-3-carboxylic acid · ligand · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1055 | 0.85 | 0.86 | 99 | WY5 |
| 2 | 1149 | 0.85 | 0.86 | 92 | empty |
| 3 | 198 | 0.68 | 0.86 | 30 | empty |
| 4 | 156 | 0.62 | 0.85 | 24 | empty |
| 5 | 145 | 0.61 | 0.85 | 18 | empty |
Interfaces
6 interfaces between chains.
- B–C · 1402 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 1385 Ų buried · 15 hydrogen bonds · protein-protein
- B–D · 1275 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 1256 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 18 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 6JNO · RXRa structure complexed with CU-6PMN · 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
- Elsewhere: RCSB PDB 6JNO · PDBe 6JNO · UniProt P19793
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