4NND

Structural basis of PTPN18 fingerprint on distinct HER2 tyrosine phosphorylation sites

• PDB DOI: https://doi.org/10.2210/pdb4NND/pdb

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


• Deposited: 2013-11-17 Released: 2014-11-19 
• Deposition Author(s): Wang, H., Yang, F., Yang, D., Du, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.291 
• R-Value Work: 0.262 
• R-Value Observed: 0.264 

Literature

Structural basis of PTPN18 fingerprint on distinct HER2 tyrosine phosphorylation sites

Wang, H., Yang, F., Yang, D., Du, Y.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 3 generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 4 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 135.81 kDa 
• Atom Count: 9,330 
• Modelled Residue Count: 1,147 
• Deposited Residue Count: 1,184 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine-protein phosphatase non-receptor type 18	A, C [auth B], E [auth D], G	290	Homo sapiens	Mutation(s): 1  Gene Names: PTPN18, BDP1 EC: 3.1.3.48
UniProt & NIH Common Fund Data Resources
Find proteins for Q99952 (Homo sapiens) Explore Q99952  Go to UniProtKB:  Q99952
PHAROS:  Q99952 GTEx:  ENSG00000072135

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Receptor tyrosine-protein kinase erbB-2	B [auth F], D [auth C], F [auth E], H	6	Homo sapiens	Mutation(s): 0  EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P04626 (Homo sapiens) Explore P04626  Go to UniProtKB:  P04626
PHAROS:  P04626 GTEx:  ENSG00000141736

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PTR	B [auth F], D [auth C], F [auth E], H	L-PEPTIDE LINKING	C9 H12 N O6 P		TYR

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.291 
• R-Value Work: 0.262 
• R-Value Observed: 0.264 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.102	α = 90
b = 95.284	β = 94.02
c = 88.161	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHENIX	model building
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-11-19 
Deposition Author(s): Wang, H., Yang, F., Yang, D., Du, Y.

Revision History  

• Version 1.0: 2014-11-19
  Type: Initial release
  
• Version 1.1: 2024-10-09
  Changes: Data collection, Database references, Derived calculations, Structure summary