8XN8

The Crystal Structure of SRC from Biortus.

• PDB DOI: https://doi.org/10.2210/pdb8XN8/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Mus musculus
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2023-12-29 Released: 2024-01-24 
• Deposition Author(s): Wang, F., Cheng, W., Yuan, Z., Lin, D., Bao, C.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.224 
• R-Value Work: 0.185 

Starting Model: experimental

Literature

The Crystal Structure of SRC from Biortus.

Wang, F., Cheng, W., Yuan, Z., Lin, D., Bao, C.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 52.23 kDa 
• Atom Count: 4,098 
• Modelled Residue Count: 450 
• Deposited Residue Count: 451 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Proto-oncogene tyrosine-protein kinase Src	A	451	Mus musculus	Mutation(s): 0  Gene Names: Src EC: 2.7.10.2
UniProt & NIH Common Fund Data Resources
Find proteins for P05480 (Mus musculus) Explore P05480  Go to UniProtKB:  P05480
IMPC:  MGI:98397

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP (Subject of Investigation/LOI)	B [auth A]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
GOL (Subject of Investigation/LOI)	D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO (Subject of Investigation/LOI)	E [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PTR	A	L-PEPTIDE LINKING	C9 H12 N O6 P		TYR

Binding Affinity Annotations
ID	Source	Binding Affinity
PTR	BindingDB:  8XN8	-TΔS: -1.81e+1 (kJ/mol) from 1 assay(s)
		ΔG: -2.14e+1 (kJ/mol) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.224 
• R-Value Work: 0.185 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.204	α = 90
b = 87.468	β = 90
c = 105.802	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-01-24 
Deposition Author(s): Wang, F., Cheng, W., Yuan, Z., Lin, D., Bao, C.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-01-24
  Type: Initial release
  
• Version 1.1: 2024-11-13
  Changes: Structure summary