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), 0.179 (DCC)
R-Value Observed:
0.179 (Depositor)

Starting Model: experimental
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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

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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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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

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), 0.179 (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

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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.