1H9U: Retinoid X receptor, beta

The structure of the human retinoid-X-receptor beta ligand binding domain in complex with the specific synthetic agonist LG100268. Determined by X-ray diffraction at 2.7 Å resolution. Released 3 Apr 2002.

Method: X-ray diffraction
Resolution: 2.7 Å
Organism: HOMO SAPIENS
Chains: 4
Atoms: 6,338
Mol. weight: 101.13 kDa
Ligands: NI, LG2
Released: 3 Apr 2002

Explore 1H9U in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1H9U contains 56 α-helices and 8 β-strands across 4 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.

Chains A, B and C: 14 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	301-309	9
α-helix	336-347	12
α-helix	350-355	6
α-helix	360-362	3
α-helix	365-387	23
β-strand	394-396	3	1
β-strand	402-404	3	1
α-helix	405-411	7
α-helix	414-419	6
α-helix	420-425	6
α-helix	426-431	6
α-helix	435-446	12
α-helix	457-478	22
α-helix	485-490	6
α-helix	493-513	21
α-helix	517-521	5

Chain D: 14 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	301-309	9
α-helix	336-347	12
α-helix	350-355	6
α-helix	360-362	3
α-helix	365-387	23
β-strand	394-396	3	4
β-strand	402-404	3	4
α-helix	405-410	6
α-helix	414-419	6
α-helix	420-425	6
α-helix	426-431	6
α-helix	435-446	12
α-helix	457-478	22
α-helix	485-490	6
α-helix	493-513	21
α-helix	517-520	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Retinoid X receptor, beta	A, B, C, D	protein	224	HOMO SAPIENS	P28702 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>1H9U_1 RETINOID X RECEPTOR, BETA (chains A, B, C, D)
MPVDRILEAELAVEQKSDQGVEGPGGTGGSGSSPNDPVTNICQAADKQLFTLVEWAKRIP
HFSSLPLDDQVILLRAGWNELLIASFSHRSIDVRDGILLATGLHVHRNSAHSAGVGAIFD
RVLTELVSKMRDMRMDKTELGCLRAIILFNPDAKGLSNPSEVEVLREKVYASLETYCKQK
YPEQQGRFAKLLLRLPALRSIGLKCLEHLFFFKLIGDTPIDTFL

Ligands and cofactors

ID	Name	Formula	Copies
NI	Nickel (II) ion	Ni	4
LG2	6-[1-(3,5,5,8,8-pentamethyl-5,6,7,8-tetrahydronaphthalen-2-yl)cyclopropyl]pyrid…	C24 H29 N O2	4

Water and common crystallization additives (CL) are not listed.

Primary citation

The Structural Basis for the Specificity of Retinoid-X Receptor-Selective Agonists: New Insights Into the Role of Helix H12. Love, J.D., Gooch, J.T., Benko, S. et al. J Biol Chem (2002) 277:11385. DOI 10.1074/JBC.M110869200 · PubMed

Other PDB entries of the same protein (UniProt P28702 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7A78 1.72 Å, Crystal structure of RXR beta LBD in complexes with palmitic acid and GRIP-1 peptide
5KYA 2.6 Å, Brain penetrant liver X receptor (LXR) modulators based on a…
5HJP 2.6 Å, Identification of LXRbeta selective agonists for the treatment of Alzheimer's Disease
5I4V 2.61 Å, Discovery of novel, orally efficacious Liver X Receptor (LXR) beta agonists
5KYJ 2.8 Å, Brain penetrant liver X receptor (LXR) modulators based on a…
1UHL 2.9 Å, Crystal structure of the LXRalfa-RXRbeta LBD heterodimer

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