9GFE: HRAR LBD protein

hRAR LBD protein in complex with AM580 agonist ligand and a stapled peptide. Determined by X-ray diffraction at 1.58 Å resolution. Released 22 Jan 2025.

Method: X-ray diffraction
Resolution: 1.58 Å
Organisms: Homo sapiens, synthetic construct
Chains: 2
Atoms: 2,138
Mol. weight: 28.14 kDa
Ligands: EQN
Released: 22 Jan 2025

Explore 9GFE in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9GFE contains 15 α-helices and 5 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: 14 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	184-196	13
α-helix	202-204	3
β-strand	208	1	1
α-helix	222-244	23
α-helix	249-251	3
α-helix	254-275	22
β-strand	277-278	2	2
β-strand	283-285	3	2
β-strand	290	1	1
β-strand	291-293	3	2
α-helix	294-297	4
α-helix	298-302	5
α-helix	303-305	3
α-helix	306-316	11
α-helix	317-319	3
α-helix	323-334	12
α-helix	345-366	22
α-helix	373-401	29
α-helix	408-414	7

Chain B: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	4-10	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Retinoic acid receptor alpha	A	protein	235	Homo sapiens	P10276 (AlphaFold model)
Stapled peptide-like ligand	B	protein	11	synthetic construct

Sequence of entity 1 (A), FASTA

>9GFE_1 Retinoic acid receptor alpha (chains A)
TPEVGELIEKVRKAHQETFPALCQLGKYTTNNSSEQRVSLDIDLWDKFSELSTKCIIKTV
EFAKQLPGFTTLTIADQITLLKAACLDILILRICTRYTPEQDTMTFSDGLTLNRTQMHNA
GFGPLTDLVFAFANQLLPLEMDDAETGLLSAICLICGDRQDLEQPDRVDMLQEPLLEALK
VYVRKRRPSRPHMFPKMLMKITDLRSISAKGAERVITLKMEIPGSMPPLIQEMLE

Sequence of entity 2 (B), FASTA

>9GFE_2 Stapled peptide-like ligand (chains B)
XAHLILHRLLA

Ligands and cofactors

ID	Name	Formula	Copies
EQN	4-{[(5,5,8,8-tetramethyl-5,6,7,8-tetrahydronaphthalen-2-yl)carbonyl]amino}benzo…	C22 H25 N O3	1

Primary citation

Guanidinium-Stapled Helical Peptides for Targeting Protein-Protein Interactions. Perdriau, C., Luton, A., Zimmeter, K. et al. Angew Chem Int Ed Engl (2025) 64:e202416348-e202416348. DOI 10.1002/anie.202416348 · PubMed

Other PDB entries of the same protein (UniProt P10276 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1DSZ 1.7 Å, Structure of the rxr/rar DNA-binding domain heterodimer in complex with the retinoic…
3KMR 1.8 Å, Crystal structure of RARalpha ligand binding domain in complex with an agonist ligand…
5K13 1.85 Å, Crystal structure of the RAR alpha ligand-binding domain in complex with an antagonist
7WQQ 1.9 Å, Retinoic acid receptor alpha mutant - N299H
3KMZ 2.1 Å, Crystal structure of RARalpha ligand binding domain in complex with the inverse agonist…
9GFI 2.1 Å, hRAR alpha LBD-AM580 complex with staple peptide
6XWG 2.4 Å, Crystal Structure of the Human RXR/RAR DNA-Binding Domain Heterodimer Bound to the Human…
7APO 2.4 Å, Crystal structure of RARalpha ligand binding domain in complex with a fragment of the…
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…
3A9E 2.75 Å, Crystal structure of a mixed agonist-bound RAR-alpha and antagonist-bound RXR-alpha…
4DQM 2.75 Å, Revealing a marine natural product as a novel agonist for retinoic acid receptors with a…

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