Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 18564.91 
• Atom Count: 1227 
• Residue Count: 170 
• Unique protein chains: 2

1OBY

Crystal structure of the complex of PDZ2 of syntenin with a syndecan-4 peptide.

• DOI: 10.2210/pdb1OBY/pdb

• Classification: CELL ADHESION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21


• Deposited: 2003-01-31 Released: 2003-07-11 
• Deposition Author(s): Kang, B.S., Cooper, D.R., Devedjiev, Y., Derewenda, U., Derewenda, Z.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.226 
• R-Value Work: 0.175 

Literature

Molecular Roots of Degenerate Specificity in Syntenin'S Pdz2 Domain: Reassessment of the Pdz Recognition Paradigm

Kang, B.S., Cooper, D.R., Devedjiev, Y., Derewenda, U., Derewenda, Z.S.

(2003) Structure 11: 845

• PubMed: 12842047 
• Primary Citation of Related Structures:  
  1OBZ, 1OBX, 1NTE


• PubMed Abstract: 
  

Crystal structures of the PDZ2 domain of the scaffolding protein syntenin, both unbound and in complexes with peptides derived from C termini of IL5 receptor (alpha chain) and syndecan, reveal the molecular roots of syntenin's degenerate specificity. Three distinct binding sites (S(0), S(-1), and S(-2)), with affinities for hydrophobic side chains, function in a combinatorial way: S(-1) and S(-2) act together to bind syndecan, while S(0) and S(-1) are involved in the binding of IL5Ralpha. Neither mode of interaction is consistent with the prior classification scheme, which defined the IL5Ralpha interaction as class I (-S/T-X-phi) and the syndecan interaction as class II (-phi-X-phi). These results, in conjunction with other emerging structural data on PDZ domains, call for a revision of their classification and of the existing model of their mechanism.

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Organizational Affiliation: 

Department of Molecular Physiology and Biological Physics, The Cancer Center, University of Virginia, Charlottesville, VA 22908, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
SYNTENIN 1	A, B	79	Homo sapiens	Mutation(s): 0  Gene Names: SDCBP (MDA9, SYCL)
Find proteins for O00560 (Homo sapiens) Go to Gene View: SDCBP Go to UniProtKB:  O00560

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
SYNDECAN-4	P, Q	6	Homo sapiens	Mutation(s): 0  Gene Names: SDC4
Find proteins for P31431 (Homo sapiens) Go to Gene View: SDC4 Go to UniProtKB:  P31431

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
SO4	A, B	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.226 
• R-Value Work: 0.175 
• Space Group: C 1 2 1

Unit Cell:

Length (Å)	Angle (°)
a = 58.337	α = 90.00
b = 54.441	β = 98.65
c = 50.219	γ = 90.00

Software Package:

Software Name	Purpose
REFMAC	refinement
AMoRE	phasing
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-01-31 
• Released Date: 2003-07-11 
• Deposition Author(s): Kang, B.S., Cooper, D.R., Devedjiev, Y., Derewenda, U., Derewenda, Z.S.

Revision History 

• Version 1.0: 2003-07-11
  Type: Initial release
• Version 1.1: 2011-05-08
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance
• Version 1.3: 2019-05-08
  Type: Data collection, Experimental preparation, Other
• Version 1.4: 2019-10-16
  Type: Data collection, Other