2FBM | pdb_00002fbm

Acetyltransferase domain of CDY1

• PDB DOI: https://doi.org/10.2210/pdb2FBM/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2005-12-09 Released: 2005-12-27 
• Deposition Author(s): Min, J.R., Antoshenko, T., Hong, W., Loppnau, P., Weigelt, J., Sundstrom, M., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Plotnikov, A.N., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.28 Å
• R-Value Free: 
  0.253 (Depositor), 0.186 (DCC) 
• R-Value Work: 
  0.187 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.191 (Depositor) 

Literature

Crystal Structure of Acetyltransferases domain of Human Testis-specific chromodomain protein Y 1

Min, J.R., Antoshenko, T., Hong, W., Loppnau, P., Weigelt, J., Sundstrom, M., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Plotnikov, A.N., Structural Genomics Consortium (SGC)

To be published.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 96.75 kDa 
• Atom Count: 6,076 
• Modeled Residue Count: 751 
• Deposited Residue Count: 873 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Y chromosome chromodomain protein 1, telomeric isoform b	A, B, C	291	Homo sapiens	Mutation(s): 0  Gene Names: CDY1 EC: 2.3.1.48
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y6F8 (Homo sapiens) Explore Q9Y6F8  Go to UniProtKB:  Q9Y6F8
PHAROS:  Q9Y6F8 GTEx:  ENSG00000172288 ENSG00000172352

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	D [auth A], E [auth B], F [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.28 Å
• R-Value Free:  0.253 (Depositor), 0.186 (DCC) 
• R-Value Work:  0.187 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.191 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 115.925	α = 90
b = 133.767	β = 90
c = 122.629	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-12-27 
Deposition Author(s): Min, J.R., Antoshenko, T., Hong, W., Loppnau, P., Weigelt, J., Sundstrom, M., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Plotnikov, A.N., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2005-12-27
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.3: 2024-02-14
  Changes: Data collection, Database references, Derived calculations