1PTU | pdb_00001ptu

CRYSTAL STRUCTURE OF PROTEIN TYROSINE PHOSPHATASE 1B COMPLEXED WITH PHOSPHOTYROSINE-CONTAINING HEXA-PEPTIDE (DADEPYL-NH2)

• PDB DOI: https://doi.org/10.2210/pdb1PTU/pdb

• Classification: COMPLEX (HYDROLASE/PEPTIDE)
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 1995-04-21 Released: 1996-08-01 
• Deposition Author(s): Barford, D., Jia, Z.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Work: 
  0.199 (Depositor) 
• R-Value Observed: 
  0.199 (Depositor) 

Literature

Structural basis for phosphotyrosine peptide recognition by protein tyrosine phosphatase 1B.

Jia, Z., Barford, D., Flint, A.J., Tonks, N.K.

(1995) Science 268: 1754-1758

• PubMed: 7540771 
• DOI: https://doi.org/10.1126/science.7540771
• Primary Citation Related Structures: 
  1PTT, 1PTU, 1PTV


• PubMed Abstract: 
  

  The crystal structures of a cysteine-215-->serine mutant of protein tyrosine phosphatase 1B complexed with high-affinity peptide substrates corresponding to an autophosphorylation site of the epidermal growth factor receptor were determined. Peptide binding to the protein phosphatase was accompanied by a conformational change of a surface loop that created a phosphotyrosine recognition pocket and induced a catalytically competent form of the enzyme. The phosphotyrosine side chain is buried within the period and anchors the peptide substrate to its binding site. Hydrogen bonds between peptide main-chain atoms and the protein contribute to binding affinity, and specific interactions of acidic residues of the peptide with basic residues on the surface of the enzyme confer sequence specificity.

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Organizational Affiliation: 
• Laboratory of Molecular Biophysics, University of Oxford, UK.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 38.17 kDa 
• Atom Count: 2,553 
• Modeled Residue Count: 304 
• Deposited Residue Count: 328 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN TYROSINE PHOSPHATASE 1B	A	321	Homo sapiens	Mutation(s): 1  EC: 3.1.3.48
UniProt & NIH Common Fund Data Resources
Find proteins for P18031 (Homo sapiens) Explore P18031  Go to UniProtKB:  P18031
PHAROS:  P18031 GTEx:  ENSG00000196396

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PHOSPHOTYROSINE-CONTAINING HEXA-PEPTIDE	B	7	N/A	Mutation(s): 0

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PTR	B	L-PEPTIDE LINKING	C9 H12 N O6 P		TYR

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Work:  0.199 (Depositor) 
• R-Value Observed: 0.199 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.4	α = 90
b = 88.4	β = 90
c = 123.6	γ = 120

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
DENZO	data reduction
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1996-08-01 
Deposition Author(s): Barford, D., Jia, Z.

Revision History  

• Version 1.0: 1996-08-01
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-11-03
  Changes: Database references, Derived calculations, Other
• Version 1.4: 2024-10-30
  Changes: Data collection, Structure summary