9SMQ | pdb_00009smq

Crystal structure of LRH-1/TIF-2 peptide in complex with CP4

• PDB DOI: https://doi.org/10.2210/pdb9SMQ/pdb

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


• Deposited: 2025-09-08 Released: 2025-10-15 
• Deposition Author(s): Kim, Y., Ildefeld, N., Heering, J., Proschak, E., Knapp, S., Kraemer, A., Structural Genomics Consortium (SGC)
• Funding Organization(s): Innovative Medicines Initiative

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.244 (Depositor), 0.212 (DCC) 
• R-Value Work: 
  0.214 (Depositor), 0.224 (DCC) 
• R-Value Observed: 
  0.216 (Depositor) 

Literature

Crystal structure of LRH-1/TIF-2 peptide in complex with CP4

Kim, Y., Ildefeld, N., Heering, J., Proschak, E., Knapp, S., Kraemer, A., Structural Genomics Consortium (SGC)

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A1B1C1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 32.34 kDa 
• Atom Count: 2,181 
• Modeled Residue Count: 265 
• Deposited Residue Count: 274 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear receptor subfamily 5 group A member 2	A	246	Homo sapiens	Mutation(s): 0  Gene Names: NR5A2, B1F, CPF, FTF
UniProt & NIH Common Fund Data Resources
Find proteins for O00482 (Homo sapiens) Explore O00482  Go to UniProtKB:  O00482
PHAROS:  O00482 GTEx:  ENSG00000116833

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear receptor coactivator 2	B [auth C], C [auth E]	14	Homo sapiens	Mutation(s): 0  Gene Names: NCOA2, BHLHE75, SRC2, TIF2
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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1JOT (Subject of Investigation/LOI)	D [auth A]	3-[5-phenyl-1-[3-(trifluoromethyl)phenyl]pyrazol-3-yl]propanoic acid C19 H15 F3 N2 O2 HDOULFPBAFNSDF-UHFFFAOYSA-N
PO4	E [auth A], F [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.244 (Depositor), 0.212 (DCC) 
• R-Value Work:  0.214 (Depositor), 0.224 (DCC) 
• R-Value Observed: 0.216 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.95	α = 90
b = 68.375	β = 90
c = 82.77	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
xia2	data reduction
MOLREP	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-10-15 
Deposition Author(s): Kim, Y., Ildefeld, N., Heering, J., Proschak, E., Knapp, S., Kraemer, A., Structural Genomics Consortium (SGC)

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Funding Organization	Location	Grant Number
Innovative Medicines Initiative	Switzerland	875510

Revision History  

• Version 1.0: 2025-10-15
  Type: Initial release