3KMR: RARalpha ligand binding domain

Crystal structure of RARalpha ligand binding domain in complex with an agonist ligand (Am580) and a coactivator fragment. Determined by X-ray diffraction at 1.8 Å resolution. Released 2 Jun 2010.

Method: X-ray diffraction
Resolution: 1.8 Å
Organism: Homo sapiens
Chains: 2
Atoms: 2,087
Mol. weight: 31.91 kDa
Ligands: EQN
Released: 2 Jun 2010

Explore 3KMR in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3KMR 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	183-196	14
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 C: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	630-637	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Retinoic acid receptor alpha	A	protein	266	Homo sapiens	P10276 (AlphaFold model)
Nuclear receptor coactivator 1	C	protein	13		Q15788 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>3KMR_1 Retinoic acid receptor alpha (chains A)
MGSSHHHHHHSSGLVPRGSHESYTLTPEVGELIEKVRKAHQETFPALCQLGKYTTNNSSE
QRVSLDIDLWDKFSELSTKCIIKTVEFAKQLPGFTTLTIADQITLLKAACLDILILRICT
RYTPEQDTMTFSDGLTLNRTQMHNAGFGPLTDLVFAFANQLLPLEMDDAETGLLSAICLI
CGDRQDLEQPDRVDMLQEPLLEALKVYVRKRRPSRPHMFPKMLMKITDLRSISAKGAERV
ITLKMEIPGSMPPLIQEMLENSEGLD

Sequence of entity 2 (C), FASTA

>3KMR_2 Nuclear receptor coactivator 1 (chains C)
RHKILHRLLQEGS

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

A unique secondary-structure switch controls constitutive gene repression by retinoic acid receptor. le Maire, A., Teyssier, C., Erb, C. et al. Nat Struct Mol Biol (2010) 17:801-807. DOI 10.1038/nsmb.1855 · PubMed

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

9GFE 1.58 Å, hRAR LBD protein in complex with AM580 agonist ligand and a stapled peptide
1DSZ 1.7 Å, Structure of the rxr/rar DNA-binding domain heterodimer in complex with the retinoic…
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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