8X5K

The Crystal Structure of SYK from Biortus.

• PDB DOI: https://doi.org/10.2210/pdb8X5K/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2023-11-17 Released: 2023-12-27 
• Deposition Author(s): Wang, F., Cheng, W., Yuan, Z., Qi, J., Shen, Z.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.244 
• R-Value Work: 0.189 

Starting Model: experimental

Literature

The Crystal Structure of SYK from Biortus.

Wang, F., Cheng, W., Yuan, Z., Qi, J., Shen, Z.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 33.01 kDa 
• Atom Count: 2,315 
• Modelled Residue Count: 264 
• Deposited Residue Count: 280 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine-protein kinase SYK	A	280	Homo sapiens	Mutation(s): 0  Gene Names: SYK EC: 2.7.10.2
UniProt & NIH Common Fund Data Resources
Find proteins for P43405 (Homo sapiens) Explore P43405  Go to UniProtKB:  P43405
PHAROS:  P43405 GTEx:  ENSG00000165025

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
3YT (Subject of Investigation/LOI)	B [auth A]	2-{[(1R,2S)-2-aminocyclohexyl]amino}-4-{[3-(2H-1,2,3-triazol-2-yl)phenyl]amino}pyrimidine-5-carboxamide C19 H23 N9 O TXGKRVFSSHPBAJ-JKSUJKDBSA-N
EDO	C [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.244 
• R-Value Work: 0.189 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.095	α = 90
b = 83.903	β = 101.519
c = 39.962	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: 2023-12-27 
Deposition Author(s): Wang, F., Cheng, W., Yuan, Z., Qi, J., Shen, Z.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2023-12-27
  Type: Initial release