5HDY

The third PDZ domain from the synaptic protein PSD-95

• PDB DOI: https://doi.org/10.2210/pdb5HDY/pdb

• Classification: PEPTIDE BINDING PROTEIN
• Organism(s): Rattus norvegicus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-01-05 Released: 2017-01-11 
• Deposition Author(s): White, K.I., Raman, A.S., Ranganathan, R.
• Funding Organization(s): Robert A. Welch Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.220 
• R-Value Work: 0.186 
• R-Value Observed: 0.190 

Starting Model: experimental

Literature

The third PDZ domain from the synaptic protein PSD-95

White, K.I., Raman, A.S., Ranganathan, R.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content

• Total Structure Weight: 12.83 kDa 
• Atom Count: 1,223 
• Modelled Residue Count: 117 
• Deposited Residue Count: 119 
• Unique protein chains: 1

Macromolecules

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	B [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.220 
• R-Value Work: 0.186 
• R-Value Observed: 0.190 
• Space Group: P 4₁ 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.657	α = 90
b = 89.657	β = 90
c = 89.657	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-01-11 
Deposition Author(s): White, K.I., Raman, A.S., Ranganathan, R.

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Funding Organization	Location	Grant Number
Robert A. Welch Foundation	United States	I-1366

Revision History  

• Version 1.0: 2017-01-11
  Type: Initial release
  
• Version 1.1: 2023-09-27
  Changes: Data collection, Database references, Refinement description