4DK8: LXR ligand binding domain

Crystal structure of LXR ligand binding domain in complex with partial agonist 5. Determined by X-ray diffraction at 2.75 Å resolution. Released 21 Mar 2012.

Method: X-ray diffraction
Resolution: 2.75 Å
Organism: Homo sapiens
Chains: 4
Atoms: 4,081
Mol. weight: 61.36 kDa
Ligands: 0KT, CA
Released: 21 Mar 2012

Explore 4DK8 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4DK8 contains 23 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: 10 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	222-241	20
α-helix	262-287	26
α-helix	292-294	3
α-helix	297-318	22
β-strand	320-321	2	1
β-strand	326-328	3	1
β-strand	334-335	2	1
α-helix	337-342	6
α-helix	347-362	16
α-helix	367-378	12
α-helix	389-410	22
α-helix	417-443	27
α-helix	451-457	7

Chains B and D: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	367-374	8

Chain C: 11 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	222-237	16
α-helix	250-253	4
α-helix	265-288	24
α-helix	292-294	3
α-helix	297-318	22
β-strand	320-321	2	2
β-strand	326-328	3	2
β-strand	334-336	3	2
α-helix	339-342	4
α-helix	347-361	15
α-helix	367-378	12
α-helix	389-410	22
α-helix	417-444	28
α-helix	451-457	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Oxysterols receptor LXR-beta	A, C	protein	247	Homo sapiens	P55055 (AlphaFold model)
Nuclear receptor coactivator 1	B, D	protein	12	Homo sapiens	Q15788 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>4DK8_1 Oxysterols receptor LXR-beta (chains A, C)
GSHMQLTAAQELMIQQLVAAQLQCNKRSFSDQPKVTPWPLGADPQSRDARQQRFAHFTEL
AIISVQEIVDFAKQVPGFLQLGREDQIALLKASTIEIMLLETARRYNHETECITFLKDFT
YSKDDFHRAGLQVEFINPIFEFSRAMRRLGLDDAEYALLIAINIFSADRPNVQEPGRVEA
LQQPYVEALLSYTRIKRPQDQLRFPRMLMKLVSLRTLSSVHSEQVFALRLQDKKLPPLLS
EIWDVHE

Sequence of entity 2 (B, D), FASTA

>4DK8_2 Nuclear receptor coactivator 1 (chains B, D)
DHQLLRYLLDKD

Ligands and cofactors

ID	Name	Formula	Copies
0KT	N-methyl-N-(4-{(1S)-2,2,2-trifluoro-1-hydroxy-1-[1-(2-methoxyethyl)-1H-pyrrol-2…	C22 H23 F3 N2 O4 S	2
CA	Calcium ion	Ca	6

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

Primary citation

Discovery of a new binding mode for a series of liver X receptor agonists. Kopecky, D.J., Jiao, X.Y., Fisher, B. et al. Bioorg Med Chem Lett (2012) 22:2407-2410. DOI 10.1016/j.bmcl.2012.02.028 · 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
6S4N 1.9 Å, LXRbeta ligand binding domain in comlpex 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

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