6A32

Crystal structure of PDGFRA kinase domain mutant T674I

PDB DOI: https://doi.org/10.2210/pdb6A32/pdb

Classification: ONCOPROTEIN
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): Yes

Deposited: 2018-06-14 Released: 2019-06-19
Deposition Author(s): Yan, X.E., Liang, L., Yun, C.H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.87 Å
R-Value Free: 0.240
R-Value Work: 0.204
R-Value Observed: 0.205

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of PDGFRA kinase domain mutant T674I

Yan, X.E., Liang, L., Yun, C.H.

To be published.

Macromolecule Content

Total Structure Weight: 40.6 kDa
Atom Count: 2,794
Modelled Residue Count: 336
Deposited Residue Count: 356
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Platelet-derived growth factor receptor alpha	A	356	Homo sapiens	Mutation(s): 1 Gene Names: PDGFRA, PDGFR2, RHEPDGFRA EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P16234 (Homo sapiens) Explore P16234 Go to UniProtKB: P16234
PHAROS: P16234 GTEx: ENSG00000134853
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P16234
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.87 Å
R-Value Free: 0.240
R-Value Work: 0.204
R-Value Observed: 0.205
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.194	α = 90
b = 87.604	β = 90
c = 96.332	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
DENZO	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2019-06-19

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2019-06-19
Type: Initial release
Version 1.1: 2023-11-22
Changes: Data collection, Database references, Refinement description

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.