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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.44 Å
R-Value Free:
0.275 (Depositor), 0.289 (DCC)
R-Value Work:
0.233 (Depositor), 0.238 (DCC)
R-Value Observed:
0.235 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3PZ7

This is version 1.2 of the entry. See complete history.

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.

Macromolecule Content

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

Macromolecules

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q155Q3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on 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), 0.289 (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

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2010-12-29

Deposition Author(s):

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.