4JS8 | pdb_00004js8

Crystal structure of TTK kinase domain with an inhibitor: 401348

• PDB DOI: https://doi.org/10.2210/pdb4JS8/pdb

• Classification: Transferase/Transferase Inhibitor
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-03-22 Released: 2014-03-26 
• Deposition Author(s): Qiu, W., Plotnikov, A.N., Plotnikova, O., Feher, M., Awrey, D.E., Chirgadze, N.Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.94 Å
• R-Value Free: 
  0.253 (Depositor), 0.282 (DCC) 
• R-Value Work: 
  0.231 (Depositor), 0.246 (DCC) 
• R-Value Observed: 
  0.232 (Depositor) 

Literature

Crystal structure of TTK kinase domain with an inhibitor: 401348

Qiu, W., Plotnikov, A.N., Plotnikova, O., Feher, M., Awrey, D.E., Chirgadze, N.Y.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 33.63 kDa 
• Atom Count: 2,276 
• Modeled Residue Count: 261 
• Deposited Residue Count: 281 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dual specificity protein kinase TTK	A	281	Homo sapiens	Mutation(s): 0  Gene Names: TTK, MPS1, MPS1L1 EC: 2.7.12.1
UniProt & NIH Common Fund Data Resources
Find proteins for P33981 (Homo sapiens) Explore P33981  Go to UniProtKB:  P33981
PHAROS:  P33981 GTEx:  ENSG00000112742

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1PF	B [auth A]	4-(cyclohexylmethoxy)-3-{4-[(1-methylpiperidin-4-yl)oxy]phenyl}-2H-indazole C26 H33 N3 O2 ZXTGHNQQRVHEIZ-UHFFFAOYSA-N
PEG	E [auth A], F [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4	C [auth A], D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	G [auth A], H [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
TPO	A	L-PEPTIDE LINKING	C4 H10 N O6 P		THR

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.94 Å
• R-Value Free:  0.253 (Depositor), 0.282 (DCC) 
• R-Value Work:  0.231 (Depositor), 0.246 (DCC) 
• R-Value Observed: 0.232 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.704	α = 90
b = 107.939	β = 90
c = 113.233	γ = 90

Software Package:

Software Name	Purpose
JDirector	data collection
PHASER	phasing
BUSTER	refinement
XDS	data reduction
XDS	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-03-26 
Deposition Author(s): Qiu, W., Plotnikov, A.N., Plotnikova, O., Feher, M., Awrey, D.E., Chirgadze, N.Y.

Revision History  

• Version 1.0: 2014-03-26
  Type: Initial release
  
• Version 1.1: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Structure summary