3PZ7 | pdb_00003pz7

Crystal structure of Ccd1-DIX domain

• PDB DOI: https://doi.org/10.2210/pdb3PZ7/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2010-12-14 Released: 2010-12-29 
• Deposition Author(s): Liu, Y.T., Wang, J.W., Chen, L., Wu, J.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.44 Å
• R-Value Free: 
  0.275 (Depositor), 0.292 (DCC) 
• R-Value Work: 
  0.233 (Depositor), 0.238 (DCC) 
• R-Value Observed: 
  0.235 (Depositor) 

Literature

Molecular basis of WNT Activation via the DIX-domain protein CCD1

Liu, Y.T., Dan, Q.J., Wang, J.W., Feng, Y.G., Chen, L., Liang, J., Li, Q.X., Lin, S.C., Wang, Z.X., Wu, J.W.

To be published.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 10.69 kDa 
• Atom Count: 750 
• Modelled Residue Count: 86 
• Deposited Residue Count: 91 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dixin	A	91	Homo sapiens	Mutation(s): 1
UniProt & NIH Common Fund Data Resources
Find proteins for Q155Q3 (Homo sapiens) Explore Q155Q3  Go to UniProtKB:  Q155Q3
PHAROS:  Q155Q3 GTEx:  ENSG00000150764

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	B [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.44 Å
• R-Value Free:  0.275 (Depositor), 0.292 (DCC) 
• R-Value Work:  0.233 (Depositor), 0.238 (DCC) 
• R-Value Observed: 0.235 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.576	α = 90
b = 62.576	β = 90
c = 77.722	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
SOLVE	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-12-29 
Deposition Author(s): Liu, Y.T., Wang, J.W., Chen, L., Wu, J.W.

Revision History  

• Version 1.0: 2010-12-29
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary