› 5q17

X-ray diffraction
2.1Å resolution

Ligand binding to FARNESOID-X-RECEPTOR

Released:
DOI: 10.2210/pdb5q17/pdb
PDB entry 5q17 coloured by chain, front view.
PDB entry 5q17 coloured by chain, side view.
PDB entry 5q17 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
D3R Grand Challenge 2: blind prediction of protein-ligand poses, affinity rankings, and relative binding free energies.
Gaieb Z, Liu S, Gathiaka S, Chiu M, Yang H, Shao C, Feher VA, Walters WP, Kuhn B, Rudolph MG, Burley SK, Gilson MK, Amaro RE
J Comput Aided Mol Des 32 1-20 (2018)
PMID: 29204945

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-172333 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Bile acid receptor Chain: A
Molecule details ›
Chain: A
Length: 233 amino acids
Theoretical weight: 27.1 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q96RI1 (Residues: 258-486; Coverage: 47%)
Gene names: BAR, FXR, HRR1, NR1H4, RIP14
Sequence domains: Ligand-binding domain of nuclear hormone receptor
Structure domains: Retinoid X Receptor
Nuclear receptor coactivator 2 Chain: B
Molecule details ›
Chain: B
Length: 12 amino acids
Theoretical weight: 1.46 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: Q15596 (Residues: 741-752; Coverage: 1%)
Gene names: BHLHE75, NCOA2, SRC2, TIF2

Ligands and Environments

1 bound ligand:
Ligand 9MV 1 x 9MV
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X10SA
Spacegroup: P65
Unit cell:
a: 93.94Å b: 93.94Å c: 47.798Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.22 0.218 0.267
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

11 review citations

Empirical Scoring Functions for Structure-Based Virtual Screening: Applications, Critical Aspects, and Challenges.
Guedes et al. (2018)
10 more

2 mentions without citation

D3R Grand Challenge 2: blind prediction of protein-ligand poses, affinity rankings, and relative binding free energies.
Gaieb et al. (2018)
1 more