6HXF | pdb_00006hxf

Human STK10 bound to a maleimide inhibitor

• PDB DOI: https://doi.org/10.2210/pdb6HXF/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-10-17 Released: 2018-10-31 
• Deposition Author(s): Sorrell, F.J., Salah, E., Serafim, R.A.M., Savitsky, P.A., Krojer, T., Bailey, H.J., Pinkas, D., Burgess-Brown, N.A., von Delft, F., Knapp, S., Arrowsmith, C., Bountra, C., Edwards, A.M., Elkins, J.M.
• Funding Organization(s): Wellcome Trust

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.09 Å
• R-Value Free: 
  0.219 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.190 (Depositor), 0.192 (DCC) 
• R-Value Observed: 
  0.192 (Depositor) 

Starting Model: experimental

Literature

Human STK10 bound to a maleimide inhibitor

Sorrell, F.J., Salah, E., Serafim, R.A.M., Elkins, J.M.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: SAXS

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 140.28 kDa 
• Atom Count: 9,913 
• Modeled Residue Count: 1,151 
• Deposited Residue Count: 1,208 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein kinase 10	A [auth B], B [auth A], C, D	302	Homo sapiens	Mutation(s): 0  Gene Names: STK10, LOK EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for O94804 (Homo sapiens) Explore O94804  Go to UniProtKB:  O94804
PHAROS:  O94804 GTEx:  ENSG00000072786

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
R70	E [auth B], J [auth A], L [auth C], N [auth D]	3-(2-methoxyphenyl)-4-[[4-(phenylcarbonyl)phenyl]amino]pyrrole-2,5-dione C24 H18 N2 O4 CXBAABOAUNPLDL-UHFFFAOYSA-N
EDO	F [auth B], G [auth B], H [auth B], I [auth B], M [auth C], O [auth D], P [auth D], Q [auth D]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	K [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP	A [auth B], B [auth A], C, D	L-PEPTIDE LINKING	C3 H8 N O6 P		SER
TPO	A [auth B], B [auth A], C, D	L-PEPTIDE LINKING	C4 H10 N O6 P		THR

Binding Affinity Annotations
ID	Source	Binding Affinity
R70	BindingDB:  6HXF	Ki: 600 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.09 Å
• R-Value Free:  0.219 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.190 (Depositor), 0.192 (DCC) 
• R-Value Observed: 0.192 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.84	α = 90
b = 101.67	β = 90
c = 198	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-10-31 
Deposition Author(s): Sorrell, F.J., Salah, E., Serafim, R.A.M., Savitsky, P.A., Krojer, T., Bailey, H.J., Pinkas, D., Burgess-Brown, N.A., von Delft, F., Knapp, S., Arrowsmith, C., Bountra, C., Edwards, A.M., Elkins, J.M.

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Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	--

Revision History  

• Version 1.0: 2018-10-31
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-11-20
  Changes: Structure summary