2VSP

Crystal structure of the fourth PDZ domain of PDZ domain-containing protein 1

• PDB DOI: https://doi.org/10.2210/pdb2VSP/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2008-04-28 Released: 2009-03-03 
• Deposition Author(s): Yue, W.W., Shafqat, N., Pilka, E.S., Johansson, C., Murray, J.W., Elkins, J., Roos, A., Cooper, C., Phillips, C., Salah, E., von Delft, F., Doyle, D., Edwards, A., Wikstrom, M., Arrowsmith, C., Bountra, C., Oppermann, U.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.41 Å
• R-Value Free: 
  0.267 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.215 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.217 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of the Fourth Pdz Domain of Pdz Domain-Containing Protein 1

Yue, W.W., Shafqat, N., Pilka, E.S., von Delft, F., Johansson, C., Elkins, J., Roos, A., Murray, J.W., Doyle, D., Edwards, A., Arrowsmith, C., Bountra, C., Oppermann, U.

To be published.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

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

Biological Assembly 3  

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

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

Biological Assembly 4  

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

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

Macromolecule Content

• Total Structure Weight: 39.18 kDa 
• Atom Count: 2,466 
• Modelled Residue Count: 329 
• Deposited Residue Count: 364 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PDZ DOMAIN-CONTAINING PROTEIN 1	A, B, C, D	91	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q5T2W1 (Homo sapiens) Explore Q5T2W1  Go to UniProtKB:  Q5T2W1
PHAROS:  Q5T2W1 GTEx:  ENSG00000174827

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.41 Å
• R-Value Free:  0.267 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.215 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.217 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.327	α = 90
b = 99.327	β = 90
c = 97.114	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-03-03 
Deposition Author(s): Yue, W.W., Shafqat, N., Pilka, E.S., Johansson, C., Murray, J.W., Elkins, J., Roos, A., Cooper, C., Phillips, C., Salah, E., von Delft, F., Doyle, D., Edwards, A., Wikstrom, M., Arrowsmith, C., Bountra, C., Oppermann, U.

Revision History  

• Version 1.0: 2009-03-03
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-01-24
  Changes: Database references, Structure summary
• Version 1.4: 2023-12-13
  Changes: Data collection, Database references, Other, Refinement description