7PDQ: Mutated form of RXRalpha ligand binding domain

Crystal structure of a mutated form of RXRalpha ligand binding domain in complex with LG100268 and a coactivator fragment. Determined by X-ray diffraction at 1.58 Å resolution. Released 3 Aug 2022.

Method: X-ray diffraction
Resolution: 1.58 Å
Organisms: Mus musculus, Homo sapiens
Chains: 2
Atoms: 2,120
Mol. weight: 29.22 kDa
Ligands: LG2
Released: 3 Aug 2022

Explore 7PDQ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7PDQ contains 14 α-helices and 2 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 13 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	237-245	9
α-helix	269-290	22
α-helix	294-296	3
α-helix	299-321	23
β-strand	328-330	3	1
β-strand	336-338	3	1
α-helix	339-344	6
α-helix	348-353	6
α-helix	354-359	6
α-helix	360-365	6
α-helix	369-380	12
α-helix	391-412	22
α-helix	419-424	6
α-helix	427-447	21
α-helix	454-459	6

Chain B: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	688-695	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Retinoic acid receptor RXR-alpha	A	protein	245	Mus musculus	P28700 (AlphaFold model)
Nuclear receptor coactivator 2	B	protein	13	Homo sapiens	Q15596 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>7PDQ_1 Retinoic acid receptor RXR-alpha (chains A)
GPHMSTSSANEDMPVEKILEAELAVEPKTETYVEANMGLNPSSPNDPVTNICQAADKQLF
TLVEWAKRIPHFSELPLDDQVILLRAGWNELLIASFSHESIAVKDGILLATGLHVHRNSA
HSAGVGAIFDRVLTELVSKMRDMQMDKTELGCLRAIVLFNPDSKGLSNPAEVEALREKVY
ASLEAYCKHKYPEQPGRFAKLLLRLPALRSIGLKQLEHLFFFKLIGDTPIDTFLMEMLEA
PHQAT

Sequence of entity 2 (B), FASTA

>7PDQ_2 Nuclear receptor coactivator 2 (chains B)
KHKILHRLLQDSS

Ligands and cofactors

ID	Name	Formula	Copies
LG2	6-[1-(3,5,5,8,8-pentamethyl-5,6,7,8-tetrahydronaphthalen-2-yl)cyclopropyl]pyrid…	C24 H29 N O2	1

Primary citation

Design and in vitro characterization of RXR variants as tools to investigate the biological role of endogenous rexinoids. le Maire, A., Rey, M., Vivat, V. et al. J Mol Endocrinol (2022) 69:377-390. DOI 10.1530/JME-22-0021 · PubMed

Other PDB entries of the same protein (UniProt P28700 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1DKF 2.5 Å, Crystal structure of a heterodimeric complex of rar and rxr ligand-binding domains
7AOS 2.55 Å, crystal structure of the RARalpha/RXRalpha ligand binding domain heterodimer in complex…
8J54 2.72 Å, Crystal structure of RXR/DR2 complex
3A9E 2.75 Å, Crystal structure of a mixed agonist-bound RAR-alpha and antagonist-bound RXR-alpha…
7QAA 2.76 Å, Crystal structure of RARalpha/RXRalpha ligand binding domain heterodimer in complex with…
1XDK 2.9 Å, Crystal Structure of the RARbeta/RXRalpha Ligand Binding Domain Heterodimer in Complex…
7PDT 3.3 Å, Crystal structure of a mutated form of RXRalpha ligand binding domain in complex with…

Browse structure collections

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