5Q13: Ligand binding to FARNESOID-X-RECEPTOR

Ligand binding to FARNESOID-X-RECEPTOR. Determined by X-ray diffraction at 1.9 Å resolution. Released 5 Jul 2017.

Method: X-ray diffraction
Resolution: 1.9 Å
Organism: Homo sapiens
Chains: 4
Atoms: 4,602
Mol. weight: 58.79 kDa
Ligands: 9MD
Released: 5 Jul 2017

Explore 5Q13 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5Q13 contains 26 α-helices and 0 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, 0 β-strands

Element	Residues	Length
α-helix	251-264	14
α-helix	271-279	9
α-helix	284-307	24
α-helix	312-314	3
α-helix	317-340	24
α-helix	348-356	9
α-helix	363-378	16
α-helix	383-394	12
α-helix	405-426	22
α-helix	433-444	12
α-helix	446-460	15
α-helix	467-472	6

Chain B: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	748-754	7

Chain C: 12 helices, 0 β-strands

Element	Residues	Length
α-helix	251-264	14
α-helix	268-269	2
α-helix	270-279	10
α-helix	284-307	24
α-helix	312-314	3
α-helix	317-340	24
α-helix	348-357	10
α-helix	363-378	16
α-helix	383-394	12
α-helix	405-426	22
α-helix	433-456	24
α-helix	467-472	6

Chain D: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	747-754	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Bile acid receptor	A, C	protein	233	Homo sapiens	Q96RI1 (AlphaFold model)
Coactivator peptide src-1 HD3	B, D	protein	14	Homo sapiens	Q15788 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>5Q13_1 Bile acid receptor (chains A, C)
GSHMELTPDQQTLLHFIMDSYNKQRMPQEITNKILKEAFSAEENFLILTEMATNHVQVLV
EFTKKLPGFQTLDHEDQIALLKGSAVEAMFLRSAEIFNKKLPSGHSDLLEARIRNSGISD
EYITPMFSFYKSIGELKMTQEEYALLTAIVILSPDRQYIKDREAVEKLQEPLLDVLQKLC
KIHQPENPQHFACLLGRLTELRTFNHHHAEMLMSWRVNDHKFTPLLCEIWDVQ

Sequence of entity 2 (B, D), FASTA

>5Q13_2 COACTIVATOR PEPTIDE SRC-1 HD3 (chains B, D)
KDHQLLRYLLDKDE

Ligands and cofactors

ID	Name	Formula	Copies
9MD	(2S)-2-[6-chloro-2-(4-chlorophenyl)-5-fluoro-1H-benzimidazol-1-yl]-N-cyclohexyl…	C26 H28 Cl2 F N3 O2	2

Primary citation

D3R Grand Challenge 2: blind prediction of protein-ligand poses, affinity rankings, and relative binding free energies. Gaieb, Z., Liu, S., Gathiaka, S. et al. J Comput Aided Mol Des (2018) 32:1-20. DOI 10.1007/s10822-017-0088-4 · PubMed

Other PDB entries of the same protein (UniProt Q96RI1 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6HL1 1.6 Å, Crystal Structure of Farnesoid X receptor (FXR) with bound NCoA-2 peptide and CDCA
6HL0 1.66 Å, Crystal Structure of Farnesoid X receptor (FXR) with bound NCoA-2 peptide
4OIV 1.7 Å, Structural basis for small molecule NDB as a selective antagonist of FXR
5Q0I 1.7 Å, Ligand binding to FARNESOID-X-RECEPTOR
1OSH 1.8 Å, A Chemical, Genetic, and Structural Analysis of the nuclear bile acid receptor FXR
5Q0K 1.8 Å, Ligand binding to FARNESOID-X-RECEPTOR
5Q0P 1.8 Å, Ligand binding to FARNESOID-X-RECEPTOR
5Q14 1.85 Å, Ligand binding to FARNESOID-X-RECEPTOR
5Q1E 1.85 Å, Ligand binding to FARNESOID-X-RECEPTOR
5Q0V 1.87 Å, Ligand binding to FARNESOID-X-RECEPTOR
5Q1D 1.89 Å, Ligand binding to FARNESOID-X-RECEPTOR
3BEJ 1.9 Å, Structure of human FXR in complex with MFA-1 and co-activator peptide

Browse structure collections

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