7PVW

Crystal structure of the intertwined dimer of the c-Src SH3 domain E93V-S94A-R95S-T96G-N112G-N113Y-T114N-E115H mutant

PDB DOI: https://doi.org/10.2210/pdb7PVW/pdb

Classification: PROTEIN BINDING
Organism(s): Gallus gallus
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: 1.50 Å
R-Value Free: 0.190
R-Value Work: 0.161
R-Value Observed: 0.162

wwPDB Validation 3D Report Full Report

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

Literature

The effect of the hinge loops composition in the domain swapping of the SH3 domain

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

To be published.

Macromolecule Content

Total Structure Weight: 13.46 kDa
Atom Count: 1,037
Modelled Residue Count: 119
Deposited Residue Count: 120
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(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, B	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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PG4 Query on PG4 Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A]	D [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.190
R-Value Work: 0.161
R-Value Observed: 0.162
Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.037	α = 90
b = 68.037	β = 90
c = 46.183	γ = 120

Software Package:

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

Structure Validation

View Full Validation Report

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 National Science Foundation (DBI-1832184), 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 R01GM133198.