5YXL

A ligand M binding to FXR

• PDB DOI: https://doi.org/10.2210/pdb5YXL/pdb

• Classification: NUCLEAR PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-12-05 Released: 2019-03-13 
• Deposition Author(s): Yi, L., Yong, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.24 Å
• R-Value Free: 0.223 
• R-Value Work: 0.214 
• R-Value Observed: 0.214 

Literature

A ligand M binding to FXR

Yi, L., Yong, L.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 56.39 kDa 
• Atom Count: 4,016 
• Modelled Residue Count: 445 
• Deposited Residue Count: 474 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bile acid receptor	A, C	229	Homo sapiens	Mutation(s): 0  Gene Names: NR1H4, BAR, FXR, HRR1, RIP14
UniProt & NIH Common Fund Data Resources
Find proteins for Q96RI1 (Homo sapiens) Explore Q96RI1  Go to UniProtKB:  Q96RI1
PHAROS:  Q96RI1 GTEx:  ENSG00000012504

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptide from Nuclear receptor coactivator 2	B, D	8	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q15596 (Homo sapiens) Explore Q15596  Go to UniProtKB:  Q15596
PHAROS:  Q15596 GTEx:  ENSG00000140396

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NIW	E [auth A], F [auth C]	2-methoxyethyl propan-2-yl 2,6-dimethyl-4-(3-nitrophenyl)pyridine-3,5-dicarboxylate C21 H24 N2 O7 SJJUCKCPGPCJQM-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.24 Å
• R-Value Free: 0.223 
• R-Value Work: 0.214 
• R-Value Observed: 0.214 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.509	α = 90
b = 117.341	β = 90
c = 151.137	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-03-13 
Deposition Author(s): Yi, L., Yong, L.

Revision History  

• Version 1.0: 2019-03-13
  Type: Initial release
  
• Version 1.1: 2024-03-27
  Changes: Data collection, Database references