2ZKC | pdb_00002zkc

Crystal structure of human estrogen-related receptor gamma ligand binding domain complex with bisphenol Z

• PDB DOI: https://doi.org/10.2210/pdb2ZKC/pdb

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


• Deposited: 2008-03-14 Released: 2009-03-17 
• Deposition Author(s): Matsushima, A., Kakuta, Y., Teramoto, T., Shimohigashi, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.234 (Depositor), 0.232 (DCC) 
• R-Value Work: 
  0.197 (Depositor) 
• R-Value Observed: 
  0.199 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of human estrogen-related receptor gamma ligand binding domain complex with bisphenol Z

Matsushima, A., Kakuta, Y., Teramoto, T., Shimohigashi, Y.

To be published.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 28.06 kDa 
• Atom Count: 2,153 
• Modeled Residue Count: 227 
• Deposited Residue Count: 244 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Estrogen-related receptor gamma	A	244	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P62508 (Homo sapiens) Explore P62508  Go to UniProtKB:  P62508
PHAROS:  P62508 GTEx:  ENSG00000196482

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BPZ	B [auth A]	4,4'-cyclohexane-1,1-diyldiphenol C18 H20 O2 SDDLEVPIDBLVHC-UHFFFAOYSA-N
GOL	C [auth A], D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.234 (Depositor), 0.232 (DCC) 
• R-Value Work:  0.197 (Depositor) 
• R-Value Observed: 0.199 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.839	α = 90
b = 63.839	β = 90
c = 135.894	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
BBS	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-03-17 
Deposition Author(s): Matsushima, A., Kakuta, Y., Teramoto, T., Shimohigashi, Y.

Revision History  

• Version 1.0: 2009-03-17
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description