7PVT | pdb_00007pvt

Crystal structure of the v-Src SH3 domain Q128R mutant in complex with the synthetic peptide VSL12

PDB DOI: https://doi.org/10.2210/pdb7PVT/pdb

Classification: PROTEIN BINDING
Organism(s): Rous sarcoma virus (strain Schmidt-Ruppin E), unidentified
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: 1.60 Å
R-Value Free:
0.204 (Depositor), 0.180 (DCC)
R-Value Work:
0.178 (Depositor), 0.180 (DCC)
R-Value Observed:
0.179 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of the v-Src SH3 domain Q128R mutant in complex with the synthetic peptide VSL12

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

To be published.

Macromolecule Content

Total Structure Weight: 16.56 kDa
Atom Count: 1,094
Modeled Residue Count: 131
Deposited Residue Count: 146
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine-protein kinase transforming protein Src	A, C	61	Rous sarcoma virus (strain Schmidt-Ruppin E)	Mutation(s): 1 Gene Names: V-SRC EC: 2.7.10.2
UniProt
Find proteins for P63185 (Rous sarcoma virus subgroup E (strain Schmidt-Ruppin)) Explore P63185 Go to UniProtKB: P63185
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P63185
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
VSL12	B, D	12	unidentified	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain F [auth C] MOL2 format, chain F [auth C] mmCIF format, chain F [auth C]	F [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain F [auth C] Interactions & Density Focus chain F [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.204 (Depositor), 0.180 (DCC)
R-Value Work: 0.178 (Depositor), 0.180 (DCC)
R-Value Observed: 0.179 (Depositor)

Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.227	α = 90
b = 51.227	β = 90
c = 46.34	γ = 120

Software Package:

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