4RTY | pdb_00004rty

Crystal structure of the c-Src-SH3 domain in complex with the high affinity peptide APP12

PDB DOI: https://doi.org/10.2210/pdb4RTY/pdb

Classification: PROTEIN BINDING
Organism(s): Gallus gallus, synthetic construct
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2014-11-16 Released: 2015-10-28
Deposition Author(s): Camara-Artigas, A., Bacarizo, J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.28 Å
R-Value Free:
0.137 (Depositor), 0.136 (DCC)
R-Value Work:
0.116 (Depositor), 0.117 (DCC)
R-Value Observed:
0.117 (Depositor)

Starting Model: experimental
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This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of the c-Src-SH3 domain in complex with the high affinity peptide APP12

Camara-Artigas, A.

To be published.

Macromolecule Content

Total Structure Weight: 8.41 kDa
Atom Count: 686
Modeled Residue Count: 71
Deposited Residue Count: 74
Unique protein chains: 2

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Proto-oncogene tyrosine-protein kinase Src	A	61	Gallus gallus	Mutation(s): 0 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

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
APP12 peptide	B	13	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.28 Å
R-Value Free: 0.137 (Depositor), 0.136 (DCC)
R-Value Work: 0.116 (Depositor), 0.117 (DCC)
R-Value Observed: 0.117 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.91	α = 90
b = 32.85	β = 104.45
c = 31.64	γ = 90

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2015-10-28

Deposition Author(s):

Camara-Artigas, A.

Revision History (Full details and data files)

Version 1.0: 2015-10-28
Type: Initial release
Version 1.1: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.2: 2024-11-20
Changes: Structure summary

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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.