3QLF | pdb_00003qlf

Crystal structure of the L317I mutant of the C-src tyrosine kinase domain complexed with pyrazolopyrimidine 5

PDB DOI: https://doi.org/10.2210/pdb3QLF/pdb

Classification: TRANSFERASE
Organism(s): Gallus gallus
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2011-02-02 Released: 2012-02-08
Deposition Author(s): Boubeva, R., Pernot, L., Perozzo, R., Scapozza, L.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.75 Å
R-Value Free:
0.232 (Depositor), 0.226 (DCC)
R-Value Work:
0.192 (Depositor), 0.184 (DCC)
R-Value Observed:
0.194 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

A single amino-acid dictates the dynamics of the switch between active and inactive C-src conformation

Boubeva, R., Pernot, L., Cristiani, A., Moretti, L., Berteotti, A., Perozzo, R., Gervasio, F., Scapozza, L.

To be published.

Macromolecule Content

Total Structure Weight: 66.36 kDa
Atom Count: 4,215
Modeled Residue Count: 507
Deposited Residue Count: 572
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Proto-oncogene tyrosine-protein kinase Src	A, B	286	Gallus gallus	Mutation(s): 1 Gene Names: SRC EC: 2.7.10.2
UniProt
Find proteins for P00523 (Gallus gallus) Explore P00523 Go to UniProtKB: P00523
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00523
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PD5 Query on PD5 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	1-{4-[4-amino-1-(1-methylethyl)-1H-pyrazolo[3,4-d]pyrimidin-3-yl]phenyl}-3-[3-(trifluoromethyl)phenyl]urea C₂₂ H₂₀ F₃ N₇ O LEERPLGXOHLQPF-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.75 Å
R-Value Free: 0.232 (Depositor), 0.226 (DCC)
R-Value Work: 0.192 (Depositor), 0.184 (DCC)
R-Value Observed: 0.194 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.268	α = 79.48
b = 63.495	β = 90.09
c = 73.451	γ = 89.41

Software Package:

Software Name	Purpose
PHASER	phasing
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2012-02-08

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-02-08
Type: Initial release
Version 1.1: 2023-09-13
Changes: Data collection, Database references, Derived calculations, 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.