5YXB | pdb_00005yxb

A ligand binding to FXR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 
    0.282 (Depositor), 0.290 (DCC) 
  • R-Value Work: 
    0.246 (Depositor), 0.246 (DCC) 
  • R-Value Observed: 
    0.249 (Depositor) 

wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

A ligand binding to FXR

Yi, L.Yong, L.

To be published.

Macromolecule Content 

  • Total Structure Weight: 28.64 kDa 
  • Atom Count: 1,967 
  • Modeled Residue Count: 234 
  • Deposited Residue Count: 240 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Bile acid receptor229Homo sapiensMutation(s): 0 
Gene Names: NR1H4BARFXRHRR1RIP14
UniProt & NIH Common Fund Data Resources
Find proteins for Q96RI1 (Homo sapiens)
Explore Q96RI1 
Go to UniProtKB:  Q96RI1
PHAROS:  Q96RI1
GTEx:  ENSG00000012504 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96RI1
Sequence Annotations
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Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Peptide from Nuclear receptor coactivator 211Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q15596 (Homo sapiens)
Explore Q15596 
Go to UniProtKB:  Q15596
PHAROS:  Q15596
GTEx:  ENSG00000140396 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15596
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
93O

Query on 93O



Download:Ideal Coordinates CCD File
C [auth A]2-methoxyethyl (2E)-3-phenylprop-2-en-1-yl 2,6-dimethyl-4-(3-nitrophenyl)pyridine-3,5-dicarboxylate
C27 H26 N2 O7
HUTPFIMQINDZDT-DHZHZOJOSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free:  0.282 (Depositor), 0.290 (DCC) 
  • R-Value Work:  0.246 (Depositor), 0.246 (DCC) 
  • R-Value Observed: 0.249 (Depositor) 
Space Group: P 42 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.399α = 90
b = 86.399β = 90
c = 75.106γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

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