2DX8 | pdb_00002dx8

Crystal Structure Analysis of the PHD domain of the Transcription Coactivator Pygophus

• PDB DOI: https://doi.org/10.2210/pdb2DX8/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Mus musculus
• Mutation(s): No 


• Deposited: 2006-08-24 Released: 2007-05-15 
• Deposition Author(s): Padmanabhan, B., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.255 (Depositor) 
• R-Value Work: 
  0.197 (Depositor) 
• R-Value Observed: 
  0.199 (Depositor) 

Literature

Crystal Structure Analysis of the PHD Domain of the Transcription Coactivator Pygopus

Nakamura, Y., Umehara, T., Hamana, H., Hayashizaki, Y., Inoue, M., Kigawa, T., Shirouzu, M., Terada, T., Tanaka, A., Padmanabhan, B., Yokoyama, S.

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: 14.73 kDa 
• Atom Count: 971 
• Modelled Residue Count: 120 
• Deposited Residue Count: 134 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pygopus homolog 1	A, B	67	Mus musculus	Mutation(s): 0
UniProt
Find proteins for Q9D0P5 (Mus musculus) Explore Q9D0P5  Go to UniProtKB:  Q9D0P5

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	C [auth A], D [auth A], E [auth B], F [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.255 (Depositor) 
• R-Value Work:  0.197 (Depositor) 
• R-Value Observed: 0.199 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.079	α = 90
b = 60.079	β = 90
c = 95.242	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
ADSC	data collection
MOSFLM	data reduction
SCALEPACK	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-05-15 
Deposition Author(s): Padmanabhan, B., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2007-05-15
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-03-13
  Changes: Data collection, Database references, Derived calculations