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Crystal structure of the rar alpha ligand-binding domain in complex with an antagonist

Analyse Crystal structure of the rar alpha ligand-binding domain in complex with an… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5K13
Type: protein
Length: 235 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Retinoic acid receptor alpha
UniProt: P10276
Ligands: 6Q7
Pockets: 2 · best druggability 0.79

Structure

x-ray diffraction · 1 distinct chain · 69% helix, 4% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Retinoic acid receptor alpha	protein	235	69% helix, 4% strand	P10276

Ligands and binding sites

6Q7 · 4-{5-(3-tert-butylphenyl)-1-[4-(methylsulfonyl)phenyl]-1H-pyrazol-3-yl}benzoic acid · ligand · 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.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	386	0.79	0.87	49	6Q7
2	94	0.41	0.77	18	empty

Compared structures

5K13 · Crystal structure of the RAR alpha ligand-binding domain in complex with an antagonist · the same entry in another collection · chain A against A, TM-score 1.00
P10276 · AlphaFold monomer V2.0 prediction for retinoic acid receptor alpha (P10276) · a predicted model of the same protein · chain A against A, TM-score 0.97

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 P10276
Elsewhere: RCSB PDB 5K13 · PDBe 5K13 · UniProt P10276

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