4PBX

Crystal structure of the six N-terminal domains of human receptor protein tyrosine phosphatase sigma

• PDB DOI: https://doi.org/10.2210/pdb4PBX/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2014-04-14 Released: 2014-11-12 
• Deposition Author(s): Coles, C.H., Mitakidis, N., Zhang, P., Elegheert, J., Lu, W., Stoker, A.W., Nakagawa, T., Craig, A.M., Jones, E.Y., Aricescu, A.R.
• Funding Organization(s): Medical Research Council (United Kingdom), Cancer Research UK, Wellcome Trust

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.15 Å
• R-Value Free: 0.265 
• R-Value Work: 0.234 
• R-Value Observed: 0.236 

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 64.79 kDa 
• Atom Count: 4,408 
• Modelled Residue Count: 568 
• Deposited Residue Count: 584 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Receptor-type tyrosine-protein phosphatase S	A	584	Homo sapiens	Mutation(s): 0  Gene Names: PTPRS EC: 3.1.3.48
UniProt & NIH Common Fund Data Resources
Find proteins for Q13332 (Homo sapiens) Explore Q13332  Go to UniProtKB:  Q13332
PHAROS:  Q13332 GTEx:  ENSG00000105426

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	B [auth A], C [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.15 Å
• R-Value Free: 0.265 
• R-Value Work: 0.234 
• R-Value Observed: 0.236 
• Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 198.78	α = 90
b = 198.78	β = 90
c = 132.4	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2014-11-12 
Deposition Author(s): Coles, C.H., Mitakidis, N., Zhang, P., Elegheert, J., Lu, W., Stoker, A.W., Nakagawa, T., Craig, A.M., Jones, E.Y., Aricescu, A.R.

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Funding Organization	Location	Grant Number
Medical Research Council (United Kingdom)	United Kingdom	G0700232
Medical Research Council (United Kingdom)	United Kingdom	G9900061
Cancer Research UK	United Kingdom	A10976
Wellcome Trust	United Kingdom	090532/Z/09/Z
Wellcome Trust	United Kingdom	DPhil Studentship for N.M.

Revision History  

• Version 1.0: 2014-11-12
  Type: Initial release
  
• Version 1.1: 2014-11-19
  Changes: Database references
• Version 1.2: 2017-08-30
  Changes: Author supporting evidence, Derived calculations
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Data collection, Derived calculations, Structure summary
• Version 1.4: 2023-12-20
  Changes: Data collection, Database references, Refinement description, Structure summary