7JYD

Human Liver Receptor Homolog-1 in Complex with 10CA and a Fragment of Tif2

  • Classification: TRANSCRIPTION
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli BL21(DE3)
  • Mutation(s): No 

  • Deposited: 2020-08-30 Released: 2022-03-02 
  • Deposition Author(s): D'Agostino, E.H., Mays, S.G., Ortlund, E.A.
  • Funding Organization(s): National Science Foundation (NSF, United States), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK), United States Department of Agriculture (USDA)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.191 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Tapping into a phospholipid-LRH-1 axis yields a powerful anti-inflammatory agent with in vivo activity against colitis

D'Agostino, E.H.Mays, S.G.Flynn, A.F.Huang, X.Wang, G.Liu, X.Millings, E.J.Okafor, C.D.Patel, A.Cato, M.L.Cornelison, J.C.Houtman, R.Moore, D.D.Calvert, J.W.Jui, N.T.Ortlund, E.A.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nuclear receptor subfamily 5 group A member 2246Homo sapiensMutation(s): 0 
Gene Names: NR5A2B1FCPFFTF
UniProt & NIH Common Fund Data Resources
Find proteins for O00482 (Homo sapiens)
Explore O00482 
Go to UniProtKB:  O00482
PHAROS:  O00482
GTEx:  ENSG00000116833 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO00482
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Nuclear receptor coactivator 2B [auth C]12Homo 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
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
VQA (Subject of Investigation/LOI)
Query on VQA

Download Ideal Coordinates CCD File 
C [auth A]10-[(3aR,6R,6aR)-6-hydroxy-3-phenyl-3a-(1-phenylethenyl)-1,3a,4,5,6,6a-hexahydropentalen-2-yl]decanoic acid
C32 H40 O3
YGTFMMNUBBGVSN-LBRLCBGXSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
VQA BindingDB:  7JYD EC50: 400 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.191 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.37α = 90
b = 88.37β = 90
c = 105.674γ = 120
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
PHENIXdata reduction
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United StatesDGE-1444932
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesT32GM008602
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)United StatesF31DK111171
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesT32GM008367-27
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)United StatesR01DK095750
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)United StatesR01DK114213
United States Department of Agriculture (USDA)United States3092-5-001-057

Revision History  (Full details and data files)

  • Version 1.0: 2022-03-02
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Data collection, Refinement description