5A2P | pdb_00005a2p

THE COMPLEX STRUCTURE OF PDZ DOMAINS IN SYNTENIN-1 WITH 4L PEPTIDE

• PDB DOI: https://doi.org/10.2210/pdb5A2P/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Rattus norvegicus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-05-21 Released: 2016-06-01 
• Deposition Author(s): Yoo, J.H., Yun, J.H., Cho, H.S., Lee, W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.244 (Depositor), 0.221 (DCC) 
• R-Value Work: 
  0.219 (Depositor), 0.232 (DCC) 
• R-Value Observed: 
  0.221 (Depositor) 

Literature

Titl the Complex Structure of Pdz Domains in Syntenin-1 with 4L Peptide

Yun, J.H., Yoo, J.H., Cho, H.S., Lee, W.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
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 PISA (software)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 74.08 kDa 
• Atom Count: 5,323 
• Modeled Residue Count: 680 
• Deposited Residue Count: 684 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SYNTENIN-1	A, B, C, D	163	Rattus norvegicus	Mutation(s): 0
UniProt
Find proteins for Q9JI92 (Rattus norvegicus) Explore Q9JI92  Go to UniProtKB:  Q9JI92

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
SYNDECAN-4	E, F, G, H	8	Rattus norvegicus	Mutation(s): 0
UniProt
Find proteins for P34901 (Rattus norvegicus) Explore P34901  Go to UniProtKB:  P34901

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.244 (Depositor), 0.221 (DCC) 
• R-Value Work:  0.219 (Depositor), 0.232 (DCC) 
• R-Value Observed: 0.221 (Depositor) 

Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.2	α = 90
b = 64.2	β = 90
c = 201.767	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-06-01 
Deposition Author(s): Yoo, J.H., Yun, J.H., Cho, H.S., Lee, W.

Revision History  

• Version 1.0: 2016-06-01
  Type: Initial release
  
• Version 1.1: 2024-05-08
  Changes: Data collection, Database references, Other