1TP5

Crystal structure of PDZ3 domain of PSD-95 protein complexed with a peptide ligand KKETWV

• PDB DOI: https://doi.org/10.2210/pdb1TP5/pdb

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


• Deposited: 2004-06-15 Released: 2005-09-20 
• Deposition Author(s): Saro, D., Wawrzak, Z., Martin, P., Vickrey, J., Paredes, A., Kovari, L., Spaller, M.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.54 Å
• R-Value Free: 
  0.229 (Depositor) 
• R-Value Work: 
  0.191 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.193 (Depositor) 

Starting Model: experimental

Literature

Structure of the third PDZ domain of PSD-95 protein complexed with KKETWV peptide ligand

Saro, D., Wawrzak, Z., Martin, P., Vickrey, J., Paredes, A., Kovari, L., Spaller, M.

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 13.53 kDa 
• Atom Count: 1,106 
• Modelled Residue Count: 121 
• Deposited Residue Count: 125 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Presynaptic density protein 95	A	119	Rattus norvegicus	Mutation(s): 0
UniProt
Find proteins for P31016 (Rattus norvegicus) Explore P31016  Go to UniProtKB:  P31016

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
LYS-LYS-GLU-THR-TRP-VAL peptide ligand	B	6	N/A	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.54 Å
• R-Value Free:  0.229 (Depositor) 
• R-Value Work:  0.191 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.193 (Depositor) 

Space Group: P 4₁ 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.978	α = 90
b = 89.978	β = 90
c = 89.978	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
XTALVIEW	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-09-20 
Deposition Author(s): Saro, D., Wawrzak, Z., Martin, P., Vickrey, J., Paredes, A., Kovari, L., Spaller, M.

Revision History  

• Version 1.0: 2005-09-20
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description
• Version 1.4: 2023-08-23
  Changes: Data collection, Database references, Refinement description