4NND | pdb_00004nnd

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.291 (Depositor), 0.278 (DCC)
R-Value Work:
0.262 (Depositor), 0.255 (DCC)
R-Value Observed:
0.264 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 4NND

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

Literature

Structural basis of PTPN18 fingerprint on distinct HER2 tyrosine phosphorylation sites

Wang, H., Yang, F., Yang, D., Du, Y.

To be published.

Macromolecule Content

Total Structure Weight: 135.81 kDa
Atom Count: 9,330
Modeled Residue Count: 1,147
Deposited Residue Count: 1,184
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 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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q99952
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

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
Entity Groups
UniProt Group	P04626
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PTR Query on 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 (Depositor), 0.278 (DCC)
R-Value Work: 0.262 (Depositor), 0.255 (DCC)
R-Value Observed: 0.264 (Depositor)

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

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Entry History

Deposition Data

Released Date: 2014-11-19

Deposition Author(s):

Revision History (Full details and data files)

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

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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.