5MKU: Retinoid X Receptor alpha

Crystal structure of the Retinoid X Receptor alpha in complex with synthetic honokiol derivative 4 and a fragment of the TIF2 co-activator. Determined by X-ray diffraction at 1.78 Å resolution. Released 8 Nov 2017.

Method: X-ray diffraction
Resolution: 1.78 Å
Organism: Homo sapiens
Chains: 2
Atoms: 2,203
Mol. weight: 27.25 kDa
Ligands: J57
Released: 8 Nov 2017

Explore 5MKU in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5MKU contains 16 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: 15 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	232-241	10
α-helix	264-284	21
α-helix	289-291	3
α-helix	294-316	23
α-helix	317-319	3
β-strand	324-325	2	1
β-strand	331-332	2	1
α-helix	334-339	6
α-helix	343-348	6
α-helix	349-354	6
α-helix	355-360	6
α-helix	364-375	12
α-helix	386-407	22
α-helix	414-419	6
α-helix	422-442	21
α-helix	446	1
α-helix	450-454	5

Chain B: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	473-480	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Retinoic acid receptor RXR-alpha	A	protein	228	Homo sapiens	P19793 (AlphaFold model)
His-lys-ile-leu-his-arg-leu-leu-gln-asp-ser	B	protein	11	Homo sapiens

Sequence of entity 1 (A), FASTA

>5MKU_1 Retinoic acid receptor RXR-alpha (chains A)
DMPVERILEAELAVEPKTETYVEANMGLNPSSPNDPVTNICQAADKQLFTLVEWAKRIPH
FSELPLDDQVILLRAGWNELLIASFSHRSIAVKDGILLATGLHVHRNSAHSAGVGAIFDR
VLTELVSKMRDMQMDKTELGCLRAIVLFNPDSKGLSNPAEVEALREKVYASLEAYCKHKY
PEQPGRFAKLLLRLPALRSIGLKCLEHLFFFKLIGDTPIDTFLMEMLE

Sequence of entity 2 (B), FASTA

>5MKU_2 HIS-LYS-ILE-LEU-HIS-ARG-LEU-LEU-GLN-ASP-SER (chains B)
HKILHRLLQDS

Ligands and cofactors

ID	Name	Formula	Copies
J57	(~{E})-3-[4-oxidanyl-3-(3-propan-2-ylphenyl)phenyl]prop-2-enoic acid	C18 H18 O3	1

Primary citation

Ligand Dependent Switch from RXR Homo- to RXR-NURR1 Heterodimerization. Scheepstra, M., Andrei, S.A., de Vries, R.M.J.M. et al. ACS Chem Neurosci (2017) 8:2065-2077. DOI 10.1021/acschemneuro.7b00216 · PubMed

Other PDB entries of the same protein (UniProt P19793 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9QX6 1.46 Å, Crystal structure of RXR alpha LBD bound to a synthetic agonist FN537 and a coactivator…
6LB4 1.5 Å, Crystal structure of dimeric RXR-LBD complexed with NEt-3ME and TIF2 co-activator
7A77 1.5 Å, Crystal structure of RXR alpha LBD in complexes with palmitic acid and GRIP-1 peptide
6FBQ 1.6 Å, Crystal Structure of the Human Retinoid X Receptor DNA-Binding Domain Bound to the Human…
9RMR 1.65 Å, Crystal structure of RXR alpha LBD bound to a synthetic agonist FN558 and a coactivator…
1DSZ 1.7 Å, Structure of the rxr/rar DNA-binding domain heterodimer in complex with the retinoic…
2P1T 1.8 Å, Crystal structure of the ligand binding domain of the retinoid X receptor alpha in…
4ZSH 1.8 Å, RXR LBD in complex with 9-cis-13,14-dihydroretinoic acid
6L6K 1.8 Å, Crystal structure of dimeric RXRalpha-LBD complexed with partial agonist CBt-PMN and SRC1
7UW2 1.88 Å, Crystal structure of human Retinoid X receptor alpha ligand binding domain complex with…
6STI 1.89 Å, Crystal structure of RXRalpha LBD in complex with LG 100754 and a coactivator peptide
1MV9 1.9 Å, Crystal Structure of the human RXR alpha ligand binding domain bound to the eicosanoid…

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