3FY5 | pdb_00003fy5

Dishevelled PDZ domain homodimer

PDB DOI: https://doi.org/10.2210/pdb3FY5/pdb

Classification: PROTEIN BINDING
Organism(s): Xenopus laevis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-01-21 Released: 2009-09-08
Deposition Author(s): Earnest, T., Friedland, N., Hung, L.-W., Moon, R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.294 (Depositor), 0.297 (DCC)
R-Value Work:
0.229 (Depositor), 0.224 (DCC)
R-Value Observed:
0.232 (Depositor)

wwPDB Validation 3D Report Full Report

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

Macromolecule Content

Total Structure Weight: 20.22 kDa
Atom Count: 1,293
Modeled Residue Count: 176
Deposited Residue Count: 182
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Segment polarity protein dishevelled homolog DVL-2	A, B	91	Xenopus laevis	Mutation(s): 0 Gene Names: dsh, dvl2
UniProt
Find proteins for P51142 (Xenopus laevis) Explore P51142 Go to UniProtKB: P51142
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P51142
Sequence Annotations Expand
Reference Sequence

Small Molecules

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.294 (Depositor), 0.297 (DCC)
R-Value Work: 0.229 (Depositor), 0.224 (DCC)
R-Value Observed: 0.232 (Depositor)

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.198	α = 90
b = 96.198	β = 90
c = 93.557	γ = 120

Software Package:

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

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2009-09-08

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2009-09-08
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2025-03-26
Changes: Data collection, Database references, Derived calculations, Structure summary

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.