5AVI: LXRalpha

Crystal structure of LXRalpha in complex with tert-butyl benzoate analog, compound 4. Determined by X-ray diffraction at 2.7 Å resolution. Released 26 Aug 2015.

Method: X-ray diffraction
Resolution: 2.7 Å
Organism: Homo sapiens
Chains: 4
Atoms: 4,097
Mol. weight: 72.19 kDa
Ligands: 4KM
Released: 26 Aug 2015

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

Secondary structure: helices and β-sheets

5AVI contains 27 α-helices and 6 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.

Chain A: 12 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	205-207	3
α-helix	208-220	13
α-helix	235-238	4
α-helix	247-274	28
α-helix	283-304	22
β-strand	306-307	2	1
β-strand	312-315	4	1
β-strand	319-321	3	1
α-helix	323-328	6
α-helix	333-349	17
α-helix	353-364	12
α-helix	375-396	22
α-helix	403-430	28
α-helix	434-436	3
α-helix	437-443	7

Chains B and D: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	688-695	8

Chain C: 13 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	205-207	3
α-helix	208-221	14
α-helix	236-238	3
α-helix	247-272	26
α-helix	283-304	22
β-strand	306-307	2	2
β-strand	312-315	4	2
β-strand	319-321	3	2
α-helix	323-328	6
α-helix	333-347	15
α-helix	353-364	12
α-helix	375-396	22
α-helix	403-408	6
α-helix	410-430	21
α-helix	434-436	3
α-helix	437-443	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Oxysterols receptor LXR-alpha	A, C	protein	283	Homo sapiens	Q13133 (AlphaFold model)
Nuclear receptor coactivator 1	B, D	protein	25	Homo sapiens	Q15788 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>5AVI_1 Oxysterols receptor LXR-alpha (chains A, C)
MKHQHQHQHQHQHQQPLQEEEQAHATSLPPRASSPPQILPQLSPEQLGMIEKLVAAQQQC
NRRSFSDRLRVTPWPMAPDPHSREARQQRFAHFTELAIVSVQEIVDFAKQLPGFLQLSRE
DQIALLKTSAIEVMLLETSRRYNPGSESITFLKDFSYNREDFAKAGLQVEFINPIFEFSR
AMNELQLNDAEFALLIAISIFSADRPNVQDQLQVERLQHTYVEALHAYVSIHHPHDRLMF
PRMLMKLVSLRTLSSVHSEQVFALRLQDKKLPPLLSEIWDVHE

Sequence of entity 2 (B, D), FASTA

>5AVI_2 Nuclear receptor coactivator 1 (chains B, D)
CPSSHSSLTERHKILHRLLQEGSPS

Ligands and cofactors

ID	Name	Formula	Copies
4KM	tert-butyl 2-[[4-[ethanoyl(methyl)amino]phenoxy]methyl]-5-(trifluoromethyl)benz…	C22 H24 F3 N O4	2

Primary citation

Discovery and structure-guided optimization of tert-butyl 6-(phenoxymethyl)-3-(trifluoromethyl)benzoates as liver X receptor agonists. Matsui, Y., Yamaguchi, T., Yamazaki, T. et al. Bioorg Med Chem Lett (2015) 25:3914-3920. DOI 10.1016/J.BMCL.2015.07.047 · PubMed

Other PDB entries of the same protein (UniProt Q13133 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5HJS 1.72 Å, Identification of LXRbeta selective agonists for the treatment of Alzheimer's Disease
3IPQ 2.0 Å, X-ray structure of GW3965 synthetic agonist bound to the LXR-alpha
3IPS 2.26 Å, X-ray structure of benzisoxazole synthetic agonist bound to the LXR-alpha
3IPU 2.4 Å, X-ray structure of benzisoxazole urea synthetic agonist bound to the LXR-alpha
5AVL 2.8 Å, Crystal structure of LXRalpha in complex with tert-butyl benzoate analog, compound 32b
1UHL 2.9 Å, Crystal structure of the LXRalfa-RXRbeta LBD heterodimer

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