Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

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

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

Macromolecule Content

• Total Structure Weight: 35.51 
• Atom Count: 2436 
• Residue Count: 275 
• Unique protein chains: 1

2CJZ

crystal structure of the c472s mutant of human protein tyrosine phosphatase ptpn5 (step, striatum enriched phosphatase) in complex with phosphotyrosine

• DOI: 10.2210/pdb2CJZ/pdb

• Classification: HYDROLASE
• Organism(s): HOMO SAPIENS
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2006-04-10 Released: 2006-05-16 
• Deposition Author(s): Debreczeni, J.E., Barr, A.J., Eswaran, J., Smee, C., Burgess, N., Gileadi, O., Savitsky, P., Sundstrom, M., Arrowsmith, C., Edwards, A., Weigelt, J., Knapp, S., von Delft, F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.205 
• R-Value Work: 0.175 
• R-Value Observed: 0.177 

Literature

Large-Scale Structural Analysis of the Classical Human Protein Tyrosine Phosphatome.

Barr, A.J., Ugochukwu, E., Lee, W.H., King, O.N.F., Filippakopoulos, P., Alfano, I., Savitsky, P., Burgess-Brown, N.A., Muller, S., Knapp, S.

(2009) Cell 136: 352

• PubMed: 19167335 
• DOI: 10.1016/j.cell.2008.11.038
• Structures With Same Primary Citation


• PubMed Abstract: 
  

Protein tyrosine phosphatases (PTPs) play a critical role in regulating cellular functions by selectively dephosphorylating their substrates. Here we present 22 human PTP crystal structures that, together with prior structural knowledge, enable a comprehensive analysis of the classical PTP family. Despite their largely conserved fold, surface properties of PTPs are strikingly diverse. A potential secondary substrate-binding pocket is frequently found in phosphatases, and this has implications for both substrate recognition and development of selective inhibitors. Structural comparison identified four diverse catalytic loop (WPD) conformations and suggested a mechanism for loop closure. Enzymatic assays revealed vast differences in PTP catalytic activity and identified PTPD1, PTPD2, and HDPTP as catalytically inert protein phosphatases. We propose a "head-to-toe" dimerization model for RPTPgamma/zeta that is distinct from the "inhibitory wedge" model and that provides a molecular basis for inhibitory regulation. This phosphatome resource gives an expanded insight into intrafamily PTP diversity, catalytic activity, substrate recognition, and autoregulatory self-association.

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Organizational Affiliation: 

University of Oxford, Structural Genomics Consortium, Old Road Campus Research Building, Roosevelt Drive, Headington, Oxford, OX3 7DQ, UK. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
HUMAN PROTEIN TYROSINE PHOSPHATASE PTPN5	A	305	HOMO SAPIENS	Mutation(s): 5  Gene Names: PTPN5 EC: 3.1.3.48
Find proteins for P54829 (Homo sapiens) Go to UniProtKB:  P54829
NIH Common Fund Data Resources
PHAROS  P54829 GTEx  ENSG00000110786

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PTR	A	O-PHOSPHOTYROSINE C9 H12 N O6 P DCWXELXMIBXGTH-QMMMGPOBSA-N
EDO	A	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.205 
• R-Value Work: 0.175 
• R-Value Observed: 0.177 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.342	α = 90
b = 64.348	β = 90
c = 100.781	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2006-04-10 
• Released Date: 2006-05-16 
Deposition Author(s): Debreczeni, J.E., Barr, A.J., Eswaran, J., Smee, C., Burgess, N., Gileadi, O., Savitsky, P., Sundstrom, M., Arrowsmith, C., Edwards, A., Weigelt, J., Knapp, S., von Delft, F.

Revision History 

• Version 1.0: 2006-05-16
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2012-06-20
  Changes: Other
• Version 1.3: 2018-01-24
  Changes: Structure summary
• Version 1.4: 2019-05-08
  Changes: Data collection, Experimental preparation
• Version 1.5: 2019-10-23
  Changes: Data collection, Database references, Other