4GFV | pdb_00004gfv

PTPN18 in complex with HER2-pY1196 phosphor-peptides

• PDB DOI: https://doi.org/10.2210/pdb4GFV/pdb

• Classification: HYDROLASE/Peptide
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 


• Deposited: 2012-08-04 Released: 2013-10-23 
• Deposition Author(s): Wang, H.M., Yang, F., Du, Y.J., Yang, D.X., Zhang, Y., Yu, X., Sun, J.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.293 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.246 (Depositor), 0.250 (DCC) 
• R-Value Observed: 
  0.248 (Depositor) 

Starting Model: experimental

Literature

PTPN18-HER2 peptides

Wang, H.M., Yang, F., Du, Y.J., Yang, D.X., Zhang, Y., Yu, X., Sun, J.P.

To be published.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 69.06 kDa 
• Atom Count: 4,816 
• Modeled Residue Count: 585 
• Deposited Residue Count: 606 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine-protein phosphatase non-receptor type 18	A, B	297	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
HER2-pY1196 phosphor-peptide	C [auth E], D [auth F]	6	Homo sapiens	Mutation(s): 0

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.293 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.246 (Depositor), 0.250 (DCC) 
• R-Value Observed: 0.248 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.348	α = 90
b = 91.341	β = 90
c = 92.97	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-10-23 
Deposition Author(s): Wang, H.M., Yang, F., Du, Y.J., Yang, D.X., Zhang, Y., Yu, X., Sun, J.P.

Revision History  

• Version 1.0: 2013-10-23
  Type: Initial release
  
• Version 1.1: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2023-12-06
  Changes: Data collection
• Version 1.3: 2024-11-27
  Changes: Structure summary