Research workbench
Rxra structure complexed with cu-6PMN and SRC1 peptide.
Analyse Rxra structure complexed with cu-6PMN and SRC1 peptide. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6JNR
- Type
- protein
- Length
- 448 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Retinoic acid receptor rxr-alpha; His-lys-ile-leu-his-arg-leu-leu-gln
- UniProt
- P19793
- Ligands
- WY5
- Pockets
- 3 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 70% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Retinoic acid receptor rxr-alpha | protein | 214 | 68% helix, 3% strand | P19793 |
| B | Retinoic acid receptor rxr-alpha | protein | 215 | 71% helix, 3% strand | P19793 |
| C | His-lys-ile-leu-his-arg-leu-leu-gln | protein | 9 | 78% helix, 0% strand | — |
| D | His-lys-ile-leu-his-arg-leu-leu-gln | protein | 10 | 70% helix, 0% strand | — |
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 · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 304 | 0.83 | 0.93 | 41 | WY5 |
| 2 | 284 | 0.83 | 0.94 | 41 | WY5 |
| 3 | 858 | 0.74 | 0.78 | 63 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1126 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 590 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 577 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 6JNR · RXRa structure complexed with CU-6PMN and SRC1 peptide. · 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 6JNR · PDBe 6JNR · UniProt P19793
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