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Crystal structure of dimeric rxralpha-lbd complexed with partial agonist cbt-pmn and SRC1
Analyse Crystal structure of dimeric rxralpha-lbd complexed with partial agonist… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6L6K
- Type
- protein
- Length
- 219 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Retinoic acid receptor rxr-alpha; Nuclear receptor coactivator 1
- EC
- 2.3.1.48
- UniProt
- P19793
- Ligands
- 9HF, CA
- Pockets
- 2 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 71% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Retinoic acid receptor rxr-alpha | protein | 210 | 71% helix, 3% strand | P19793 |
| B | Nuclear receptor coactivator 1 (EC 2.3.1.48) | protein | 9 | 78% helix, 0% strand | — |
Ligands and binding sites
- 9HF · 1-(3,5,5,8,8-pentamethyl-6,7-dihydronaphthalen-2-yl) benzotriazole-5-carboxylic acid · ligand · chains A
- CA · Calcium ion · metal · 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 | 287 | 0.82 | 0.92 | 39 | 9HF |
| 2 | 69 | 0.33 | 0.76 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 540 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 6L6K · Crystal structure of dimeric RXRalpha-LBD complexed with partial agonist CBt-PMN and SRC1 · 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 6L6K · PDBe 6L6K · UniProt P19793
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