6S4N: Oxysterols receptor LXR-beta

LXRbeta ligand binding domain in comlpex with small molecule inhibitors. Determined by X-ray diffraction at 1.9 Å resolution. Released 27 Nov 2019.

Method: X-ray diffraction
Resolution: 1.9 Å
Organism: Homo sapiens
Chains: 4
Atoms: 8,422
Mol. weight: 116.82 kDa
Ligands: KUW
Released: 27 Nov 2019

Explore 6S4N in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6S4N contains 48 α-helices and 12 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	222-241	20
α-helix	250-252	3
α-helix	261-288	28
α-helix	292-294	3
α-helix	297-318	22
β-strand	320-321	2	2
β-strand	326-329	4	2
β-strand	333-335	3	2
α-helix	337-342	6
α-helix	347-363	17
α-helix	367-378	12
α-helix	389-410	22
α-helix	417-444	28
α-helix	448-450	3
α-helix	451-456	6

Chain B: 12 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	222-242	21
α-helix	249-253	5
α-helix	263-288	26
α-helix	292-294	3
α-helix	297-318	22
β-strand	320-321	2	3
β-strand	326-329	4	3
β-strand	333-335	3	3
α-helix	337-342	6
α-helix	347-363	17
α-helix	367-378	12
α-helix	389-410	22
α-helix	417-444	28
α-helix	448-450	3
α-helix	451-457	7

Chain C: 11 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	222-243	22
α-helix	263-288	26
α-helix	292-294	3
α-helix	297-318	22
β-strand	320-321	2	4
β-strand	326-329	4	4
β-strand	333-335	3	4
α-helix	337-342	6
α-helix	347-363	17
α-helix	367-378	12
α-helix	389-409	21
α-helix	417-444	28
α-helix	448-450	3
α-helix	451-457	7

Chain D: 13 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	222-244	23
α-helix	246-248	3
α-helix	250-252	3
α-helix	261-288	28
α-helix	292-294	3
α-helix	297-318	22
β-strand	320-321	2	1
β-strand	326-329	4	1
β-strand	333-335	3	1
α-helix	337-342	6
α-helix	347-363	17
α-helix	367-378	12
α-helix	389-410	22
α-helix	417-444	28
α-helix	448-450	3
α-helix	451-457	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Oxysterols receptor LXR-beta	A, B, C, D	protein	245	Homo sapiens	P55055 (AlphaFold model)

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

>6S4N_1 Oxysterols receptor LXR-beta (chains A, B, C, D)
GVQLTAAQELMIQQLVAAQLQCNKRSFSDQPKVTPWPLGADPQSRDARQQRFAHFTELAI
ISVQEIVDFAKQVPGFLQLGREDQIALLKASTIEIMLLETARRYNHETECITFLKDFTYS
KDDFHRAGLQVEFINPIFEFSRAMRRLGLDDAEYALLIAINIFSADRPNVQEPGRVEALQ
QPYVEALLSYTRIKRPQDQLRFPRMLMKLVSLRTLSSVHSEQVFALRLQDKKLPPLLSEI
WDVHE

Ligands and cofactors

ID	Name	Formula	Copies
KUW	2-[5-chloranyl-6-[4-[[1,1,3-tris(oxidanylidene)-5-phenyl-2-propan-2-yl-1,2-thia…	C24 H27 Cl N4 O5 S	7

Water and common crystallization additives (SO4) are not listed.

Primary citation

Structural analysis identifies an escape route from the adverse lipogenic effects of liver X receptor ligands. Belorusova, A.Y., Evertsson, E., Hovdal, D. et al. Commun Biol (2019) 2:431-431. DOI 10.1038/s42003-019-0675-0 · PubMed

Other PDB entries of the same protein (UniProt P55055 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6S5K 1.6 Å, LXRbeta ligand binding domain in complex with small molecule inhibitors
6S4T 2.0 Å, LXRbeta ligand binding domain in comlpex with small molecule inhibitors
4RAK 2.04 Å, Crystal structure of nuclear receptor subfamily 1, group h, member 2 (lxrb) complexed…
1PQ9 2.1 Å, Human lxr beta hormone receptor complexed with T0901317 complex
1UPV 2.1 Å, Crystal structure of the human Liver X receptor beta ligand binding domain in complex…
3L0E 2.3 Å, X-ray crystal structure of a Potent Liver X Receptor Modulator
1PQ6 2.4 Å, Human lxr beta hormone receptor / GW3965 complex
1UPW 2.4 Å, Crystal structure of the human Liver X receptor beta ligand binding domain in complex…
3KFC 2.4 Å, Complex Structure of LXR with an agonist
5JY3 2.4 Å, Crystal structure of lxrbeta (nuclear receptor subfamily 1, group H, member 2) complexed…
4DK7 2.45 Å, Crystal structure of LXR ligand binding domain in complex with full agonist 1
6K9H 2.5 Å, Human LXR-beta in complex with an agonist

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