2VPH

Crystal structure of the human protein tyrosine phosphatase, non- receptor type 4, PDZ domain

• PDB DOI: https://doi.org/10.2210/pdb2VPH/pdb

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


• Deposited: 2008-02-29 Released: 2008-03-18 
• Deposition Author(s): Roos, A.K., Wang, J., Burgess-Brown, N., Elkins, J.M., Kavanagh, K., Pike, A.C.W., Filippakopoulos, P., Arrowsmith, C.H., Weigelt, J., Edwards, A., von Delft, F., Bountra, C., Knapp, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.243 
• R-Value Work: 0.208 
• R-Value Observed: 0.210 

Starting Models: experimental

Literature

Crystal Structure of the Human Protein Tyrosine Phosphatase, Non-Receptor Type 4, Pdz Domain

Roos, A.K., Wang, J., Burgess-Brown, N., Elkins, J.M., Kavanagh, K., Pike, A.C.W., Filippakopoulos, P., Arrowsmith, C.H., Weigelt, J., Edwards, A., von Delft, F., Bountra, C., Knapp, S.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

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.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Macromolecule Content

• Total Structure Weight: 22.08 kDa 
• Atom Count: 1,496 
• Modelled Residue Count: 190 
• Deposited Residue Count: 200 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TYROSINE-PROTEIN PHOSPHATASE NON-RECEPTOR TYPE 4	A, B	100	Homo sapiens	Mutation(s): 0  EC: 3.1.3.48
UniProt & NIH Common Fund Data Resources
Find proteins for P29074 (Homo sapiens) Explore P29074  Go to UniProtKB:  P29074
PHAROS:  P29074 GTEx:  ENSG00000088179

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.243 
• R-Value Work: 0.208 
• R-Value Observed: 0.210 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.489	α = 90
b = 71.015	β = 90
c = 71.598	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-03-18 
Deposition Author(s): Roos, A.K., Wang, J., Burgess-Brown, N., Elkins, J.M., Kavanagh, K., Pike, A.C.W., Filippakopoulos, P., Arrowsmith, C.H., Weigelt, J., Edwards, A., von Delft, F., Bountra, C., Knapp, S.

Revision History  

• Version 1.0: 2008-03-18
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2018-01-24
  Changes: Database references
• Version 1.3: 2023-12-13
  Changes: Data collection, Database references, Other, Refinement description