1RGR | pdb_00001rgr

Cyclic Peptides Targeting PDZ Domains of PSD-95: Structural Basis for Enhanced Affinity and Enzymatic Stability

• PDB DOI: https://doi.org/10.2210/pdb1RGR/pdb

• Classification: STRUCTURAL PROTEIN/DE NOVO PROTEIN
• Organism(s): Rattus norvegicus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2003-11-12 Released: 2004-05-18 
• Deposition Author(s): Piserchio, A., Salinas, G.D., Li, T., Marshall, J., Spaller, M.R., Mierke, D.F.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 22 
• Selection Criteria: structures with acceptable covalent geometry,structures with the least restraint violations 

Literature

Targeting Specific PDZ Domains of PSD-95; Structural Basis for Enhanced Affinity and Enzymatic Stability of a Cyclic Peptide.

Piserchio, A., Salinas, G.D., Li, T., Marshall, J., Spaller, M.R., Mierke, D.F.

(2004) Chem Biol 11: 469-473

• PubMed: 15123241 
• DOI: https://doi.org/10.1016/j.chembiol.2004.03.013
• Primary Citation Related Structures: 
  1RGR


• PubMed Abstract: 
  

  A cyclic peptide, Tyr-Lys-c[-Lys-Thr-Glu(betaAla)-]-Val, incorporating a beta-Ala lactam side chain linker and designed to target the PDZ domains of the postsynaptic density protein 95 (PSD-95), has been synthesized and structurally characterized by NMR while free and bound to the PDZ1 domain of PSD-95. While bound, the lactam linker of the peptide makes a number of unique contacts outside the canonical PDZ binding motif, providing a novel target for PDZ-domain specificity as well as producing a 10-fold enhancement in binding affinity. Additionally, the cyclization greatly enhances the enzymatic stability, increasing the duration that the peptide inhibits the association between PSD-95 and glutamate receptors, effectively inhibiting the clustering of kainate receptors for over 14 hr after application. Highly specific regulation of kainate receptor action may provide a novel route for treatment of drug addiction and epilepsy.

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Organizational Affiliation: 
• Department of Chemistry, Division of Biology & Medicine, Brown University, Providence, RI 02912 USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 11.72 kDa 
• Atom Count: 763 
• Modeled Residue Count: 99 
• Deposited Residue Count: 105 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Presynaptic density protein 95	A	99	Rattus norvegicus	Mutation(s): 0  Gene Names: DLG4, PSD95
UniProt
Find proteins for P31016 (Rattus norvegicus) Explore P31016  Go to UniProtKB:  P31016

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
postsynaptic protein CRIPT peptide	B	6	N/A	Mutation(s): 2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BAL	C [auth B]	BETA-ALANINE C3 H7 N O2 UCMIRNVEIXFBKS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 22 
• Selection Criteria: structures with acceptable covalent geometry,structures with the least restraint violations 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-05-18 
Deposition Author(s): Piserchio, A., Salinas, G.D., Li, T., Marshall, J., Spaller, M.R., Mierke, D.F.

Revision History  

• Version 1.0: 2004-05-18
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2021-10-27
  Changes: Data collection, Database references, Derived calculations
• Version 1.4: 2024-10-30
  Changes: Data collection, Structure summary