2FW2

Catalytic domain of CDY

• PDB DOI: https://doi.org/10.2210/pdb2FW2/pdb

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


• Deposited: 2006-01-31 Released: 2006-02-14 
• Deposition Author(s): Min, J.R., Antoshenko, T., Wu, H., Weigelt, J., Sundstrom, M., Arrowsmith, C., Edwards, A.M., Bochkarev, A., Plotnikov, A.N., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.253 
• R-Value Work: 0.185 
• R-Value Observed: 0.188 

Literature

The Crystal Structure of catalytic domain of Human Testis-specific chromodomain protein Y.

Min, J.R., Antoshenko, T., Wu, H., Weigelt, J., Sundstrom, M., Arrowsmith, C., Edwards, A.M., Bochkarev, A., Plotnikov, A.N.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 2 generated by PISA,PQS (software)

Biological Assembly 3  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 3 generated by PISA,PQS (software)

Macromolecule Content

• Total Structure Weight: 173.29 kDa 
• Atom Count: 12,641 
• Modelled Residue Count: 1,545 
• Deposited Residue Count: 1,560 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Testis-specific chromodomain protein Y 2	A, B, C, D, E, F	260	Homo sapiens	Mutation(s): 0  Gene Names: CDY2A, CDY2
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y6F7 (Homo sapiens) Explore Q9Y6F7  Go to UniProtKB:  Q9Y6F7
PHAROS:  Q9Y6F7 GTEx:  ENSG00000182415 ENSG00000129873

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.253 
• R-Value Work: 0.185 
• R-Value Observed: 0.188 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.454	α = 90
b = 133.579	β = 117.56
c = 82.328	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-02-14 
Deposition Author(s): Min, J.R., Antoshenko, T., Wu, H., Weigelt, J., Sundstrom, M., Arrowsmith, C., Edwards, A.M., Bochkarev, A., Plotnikov, A.N., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2006-02-14
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Derived calculations, Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2023-08-30
  Changes: Data collection, Database references, Refinement description