7PVX | pdb_00007pvx

Crystal structure of the c-Src SH3 domain mutant E93V-S94A-R95S-T96G-N112G-N113Y-T114N-E115H in complex with the synthetic peptide VSL12

PDB DOI: https://doi.org/10.2210/pdb7PVX/pdb

Classification: PROTEIN BINDING
Organism(s): Gallus gallus, synthetic construct
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2021-10-05 Released: 2022-09-14
Deposition Author(s): Camara-Artigas, A., Salinas Garcia, M.C.
Funding Organization(s): Ministry of Economy and Competitiveness (MINECO)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.43 Å
R-Value Free:
0.210 (Depositor), 0.177 (DCC)
R-Value Work:
0.174 (Depositor), 0.177 (DCC)
R-Value Observed:
0.176 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of the c-Src SH3 domain mutants of the specificity region in complex with polyproline peptides

Camara-Artigas, A., Salinas Garcia, M.C.

To be published.

Macromolecule Content

Total Structure Weight: 15.84 kDa
Atom Count: 1,185
Modeled Residue Count: 139
Deposited Residue Count: 144
Unique protein chains: 2

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isoform 1 of Proto-oncogene tyrosine-protein kinase Src	A, C	60	Gallus gallus	Mutation(s): 8 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

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
VSL12 peptide	B, D	12	synthetic construct	Mutation(s): 0

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.43 Å
R-Value Free: 0.210 (Depositor), 0.177 (DCC)
R-Value Work: 0.174 (Depositor), 0.177 (DCC)
R-Value Observed: 0.176 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 28.991	α = 90
b = 59.658	β = 98.62
c = 37.349	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2022-09-14

Deposition Author(s):

Camara-Artigas, A.

Salinas Garcia, M.C.

Funding Organization	Location	Grant Number
Ministry of Economy and Competitiveness (MINECO)	Spain	BIO2006-78020-R

Revision History (Full details and data files)

Version 1.0: 2022-09-14
Type: Initial release
Version 1.1: 2024-01-31
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.