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.

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), 0.249 (DCC)
R-Value Observed:
0.248 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history.

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.

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

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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 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
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 Query on 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), 0.249 (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

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Entry History

Deposition Data

Released Date: 2013-10-23

Deposition Author(s):

Revision History (Full details and data files)

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

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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.