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

Validation slider image for 3FY5

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

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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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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

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View more in-depth experimental data

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

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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.