7XTY | pdb_00007xty

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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.240 (Depositor), 0.241 (DCC)
R-Value Work:
0.194 (Depositor), 0.194 (DCC)
R-Value Observed:
0.198 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7XTY

This is version 1.1 of the entry. See complete history.

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.

Macromolecule Content

Total Structure Weight: 22.26 kDa
Atom Count: 1,563
Modeled Residue Count: 195
Deposited Residue Count: 212
Unique protein chains: 2

Macromolecules

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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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q12923
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P25054
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.240 (Depositor), 0.241 (DCC)
R-Value Work: 0.194 (Depositor), 0.194 (DCC)
R-Value Observed: 0.198 (Depositor)

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

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-05-17

Deposition Author(s):

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

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.