7XTY

Crystal Structure of the second PDZ domain from human PTPN13 in complex with APC peptide

• PDB DOI: https://doi.org/10.2210/pdb7XTY/pdb

• Classification: PEPTIDE BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2022-05-18 Released: 2023-05-17 
• Deposition Author(s): Jing, L.Q., Sun, X.N., Ma, W.H., Zhou, W.J., Wu, D.L.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.240 
• R-Value Work: 0.194 
• R-Value Observed: 0.198 

Literature

Targeting PTPN13 with 11 amino acid peptides of C-terminal APC prevents immune evasion of colorectal cancer

Jing, L.Q., Sun, X.N., Ma, W.H., Zhou, W.J., Wu, D.L.

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 Evidence: gel filtration

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: 22.26 kDa 
• Atom Count: 1,563 
• Modelled Residue Count: 195 
• Deposited Residue Count: 212 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine-protein phosphatase non-receptor type 13	A, B	95	Homo sapiens	Mutation(s): 0  Gene Names: PTPN13, PNP1, PTP1E, PTPL1 EC: 3.1.3.48
UniProt & NIH Common Fund Data Resources
Find proteins for Q12923 (Homo sapiens) Explore Q12923  Go to UniProtKB:  Q12923
PHAROS:  Q12923 GTEx:  ENSG00000163629

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
APC-peptide	C, D	11	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P25054 (Homo sapiens) Explore P25054  Go to UniProtKB:  P25054
PHAROS:  P25054 GTEx:  ENSG00000134982

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.240 
• R-Value Work: 0.194 
• R-Value Observed: 0.198 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.462	α = 90
b = 32.407	β = 108.86
c = 69.917	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
PDB_EXTRACT	data extraction
HKL-3000	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-05-17 
Deposition Author(s): Jing, L.Q., Sun, X.N., Ma, W.H., Zhou, W.J., Wu, D.L.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	22177063

Revision History  

• Version 1.0: 2023-05-17
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description