8VCG | pdb_00008vcg

Mutant Src SH2 domain in complex with phosphotyrosine

PDB DOI: https://doi.org/10.2210/pdb8VCG/pdb

Classification: PROTEIN BINDING
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2023-12-14 Released: 2025-01-29
Deposition Author(s): Hashem, A., Nyovanie, S., Oltean, N., Patskovska, L., Patskovsky, Y., Krogsgaard, M.
Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.61 Å
R-Value Free:
0.176 (Depositor), 0.182 (DCC)
R-Value Work:
0.122 (Depositor), 0.128 (DCC)
R-Value Observed:
0.124 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Engineered Mutant Src Sh2 Domain

Hashem, A., Nyovanie, S., Patskovsky, Y., Krogsgaard, M.

To be published.

Macromolecule Content

Total Structure Weight: 14.58 kDa
Atom Count: 1,029
Modeled Residue Count: 108
Deposited Residue Count: 126
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isoform 3 of Proto-oncogene tyrosine-protein kinase Src	A	126	Homo sapiens	Mutation(s): 0 Gene Names: SRC, SRC1 EC: 2.7.10.2
UniProt & NIH Common Fund Data Resources
Find proteins for P12931 (Homo sapiens) Explore P12931 Go to UniProtKB: P12931
PHAROS: P12931 GTEx: ENSG00000197122
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P12931
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PTR (Subject of Investigation/LOI) Query on PTR Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	O-PHOSPHOTYROSINE C₉ H₁₂ N O₆ P DCWXELXMIBXGTH-QMMMGPOBSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.61 Å
R-Value Free: 0.176 (Depositor), 0.182 (DCC)
R-Value Work: 0.122 (Depositor), 0.128 (DCC)
R-Value Observed: 0.124 (Depositor)

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.674	α = 90
b = 67.674	β = 90
c = 46.759	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-01-29

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	CA243486-01A1

Revision History (Full details and data files)

Version 1.0: 2025-01-29
Type: Initial release

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.