5D13 | pdb_00005d13

Third PDZ domain (PDZ3) of PSD-95 complexed with CFMOC-KKETEV peptide

• PDB DOI: https://doi.org/10.2210/pdb5D13/pdb

• Classification: signaling protein/inhibitor
• Organism(s): Rattus norvegicus, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-08-03 Released: 2016-08-17 
• Deposition Author(s): De, S., Spaller, M.R., Olson, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 
  0.257 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.210 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.212 (Depositor) 

Starting Model: experimental

Literature

Chemically-modified peptides as inhibitors of PDZ3 of PSD-95

Memic, A., De, S., Lakhani, B., Beveridge, D.L., Olson, R., Spaller, M.R.

To be published.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

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

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 55.73 kDa 
• Atom Count: 3,148 
• Modeled Residue Count: 431 
• Deposited Residue Count: 511 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Disks large homolog 4	A, B, C, D	119	Rattus norvegicus	Mutation(s): 0  Gene Names: Dlg4, Dlgh4, Psd95
UniProt
Find proteins for P31016 (Rattus norvegicus) Explore P31016  Go to UniProtKB:  P31016

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
CFMOC-KKETEV peptide	E [auth G], F [auth E], G [auth H], H [auth F], I	7	synthetic construct	Mutation(s): 0

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_002186	E, F, G, H, I	CFMOC-KKETEV peptide	Oligopeptide / Inhibitor

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free:  0.257 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.210 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.212 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.94	α = 90
b = 84.94	β = 90
c = 210.192	γ = 120

Software Package:

Software Name	Purpose
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-08-17 
Deposition Author(s): De, S., Spaller, M.R., Olson, R.

Revision History  

• Version 1.0: 2016-08-17
  Type: Initial release
  
• Version 1.1: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 2.0: 2024-04-24
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Other, Polymer sequence, Refinement description, Source and taxonomy, Structure summary
• Version 3.0: 2024-07-10
  Changes: Data collection, Non-polymer description, Structure summary
• Version 3.1: 2024-10-16
  Changes: Structure summary