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), 0.180 (DCC)
R-Value Work:
0.174 (Depositor), 0.180 (DCC)
R-Value Observed:
0.176 (Depositor)

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 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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(by identity cutoff) | 3D Structure

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% Identity50% Identity70% Identity90% Identity95% Identity100% 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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.43 Å
R-Value Free: 0.210 (Depositor), 0.180 (DCC)
R-Value Work: 0.174 (Depositor), 0.180 (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

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.