2YD3

CRYSTAL STRUCTURE OF THE N-TERMINAL IG1-2 MODULE OF HUMAN RECEPTOR PROTEIN TYROSINE PHOSPHATASE SIGMA

Structural Biology Knowledgebase: 2YD3 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.235
  • R-Value Work: 0.201

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2YD3

Classification: HYDROLASE

Total Structure Weight: 22325.61

Macromolecule Entities
Molecule Chains Length Organism Details
RECEPTOR-TYPE TYROSINE-PROTEIN PHOSPHATASE S A 202 Homo sapiens EC#: 3.1.3.48 IUBMB
Fragment: IG1-2, RESIDUES 30-228
Gene Name(s): PTPRS Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
CL
Query on CL

A CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NA
Query on NA

A SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.235
  • R-Value Work: 0.201
  • Space Group: I 41 2 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 104.22 α = 90.00
b = 104.22 β = 90.00
c = 94.85 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2011-03-17
  • Released Date: 2011-04-13
  • Deposition author(s): Coles, C.H., Shen, Y., Tenney, A.P., Siebold, C., Sutton, G.C., Lu, W., Gallagher, J.T., Jones, E.Y., Flanagan, J.G., Aricescu, A.R.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4