3FK2 | pdb_00003fk2

Crystal structure of the RhoGAP domain of human glucocorticoid receptor DNA-binding factor 1

• PDB DOI: https://doi.org/10.2210/pdb3FK2/pdb

• Classification: SIGNALING PROTEIN, HYDROLASE ACTIVATOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-12-15 Released: 2008-12-23 
• Deposition Author(s): Nedyalkova, L., Tong, Y., Tempel, W., Loppnau, P., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Weigelt, J., Bochkarev, A., Park, H., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.273 (Depositor), 0.264 (DCC) 
• R-Value Work: 
  0.223 (Depositor), 0.214 (DCC) 
• R-Value Observed: 
  0.226 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the RhoGAP domain of human glucocorticoid receptor DNA-binding factor 1

Nedyalkova, L., Tong, Y., Tempel, W., Loppnau, P., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Weigelt, J., Bochkarev, A., Park, H.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 115.52 kDa 
• Atom Count: 6,165 
• Modeled Residue Count: 780 
• Deposited Residue Count: 984 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucocorticoid receptor DNA-binding factor 1	A, B, C, D	246	Homo sapiens	Mutation(s): 0  Gene Names: GRLF1, GRF1, KIAA1722
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NRY4 (Homo sapiens) Explore Q9NRY4  Go to UniProtKB:  Q9NRY4
PHAROS:  Q9NRY4 GTEx:  ENSG00000160007

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UNX	E [auth A], F [auth A], G [auth B], H [auth B], I [auth C], J [auth C], K [auth D], L [auth D]	UNKNOWN ATOM OR ION X

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.273 (Depositor), 0.264 (DCC) 
• R-Value Work:  0.223 (Depositor), 0.214 (DCC) 
• R-Value Observed: 0.226 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 165.025	α = 90
b = 72.408	β = 90
c = 72.863	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-12-23 
Deposition Author(s): Nedyalkova, L., Tong, Y., Tempel, W., Loppnau, P., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Weigelt, J., Bochkarev, A., Park, H., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2008-12-23
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description