Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

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

Macromolecule Content

• Total Structure Weight: 18.56 kDa 
• Atom Count: 1372 
• Residue Count: 160 
• 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
• Mutation(s): No 


• 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 
• DOI: 10.1016/s0969-2126(03)00125-4
• Primary Citation of Related Structures:  
  1NTE, 1OBZ, 1OBY, 1OBX


• 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

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SYNTENIN 1	A, B	79	Homo sapiens	Mutation(s): 0  Gene Names: SDCBP, MDA9, SYCL
Find proteins for O00560 (Homo sapiens) Explore O00560  Go to UniProtKB:  O00560
NIH Common Fund Data Resources
PHAROS:  O00560 GTEx:  ENSG00000137575

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
SYNDECAN-4	P, Q	6	Homo sapiens	Mutation(s): 0  Gene Names: SDC4
Find proteins for P31431 (Homo sapiens) Explore P31431  Go to UniProtKB:  P31431
NIH Common Fund Data Resources
PHAROS:  P31431 GTEx:  ENSG00000124145

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
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
b = 54.441	β = 98.65
c = 50.219	γ = 90

Software Package:

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

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
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2019-05-08
  Changes: Data collection, Experimental preparation, Other
• Version 1.4: 2019-10-16
  Changes: Data collection, Other