8A5J | pdb_00008a5j

Crystal structure of Human STE20-like kinase 1, MST1 in complex with compound XMU-MP-1

• PDB DOI: https://doi.org/10.2210/pdb8A5J/pdb

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


• Deposited: 2022-06-15 Released: 2022-07-13 
• Deposition Author(s): Nawrotek, A., Vuillard, L., Miallau, L.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.12 Å
• R-Value Free: 
  0.248 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.243 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.243 (Depositor) 

Starting Model: other

Literature

Crystal structure of the Kelch domain of human Keap1in complex with ligand S217879

Weber, C., Vuillard, L., Delerive, P., Miallau, L.

To be published.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 64.86 kDa 
• Atom Count: 4,369 
• Modeled Residue Count: 528 
• Deposited Residue Count: 564 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein kinase 4 37kDa subunit	A, B	282	Homo sapiens	Mutation(s): 0  Gene Names: STK4, KRS2, MST1 EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q13043 (Homo sapiens) Explore Q13043  Go to UniProtKB:  Q13043
PHAROS:  Q13043 GTEx:  ENSG00000101109

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
5BS (Subject of Investigation/LOI)	C [auth A], D [auth B]	4-[(5,10-dimethyl-6-oxo-6,10-dihydro-5H-pyrimido[5,4-b]thieno[3,2-e][1,4]diazepin-2-yl)amino]benzenesulfonamide C17 H16 N6 O3 S2 YRDHKIFCGOZTGD-UHFFFAOYSA-N

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

Binding Affinity Annotations
ID	Source	Binding Affinity
5BS	BindingDB:  8A5J	IC50: min: 104, max: 1510 (nM) from 3 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.12 Å
• R-Value Free:  0.248 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.243 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.243 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 111.41	α = 90
b = 111.41	β = 90
c = 170.655	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
autoPROC	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-07-13 
Deposition Author(s): Nawrotek, A., Vuillard, L., Miallau, L.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2022-07-13
  Type: Initial release
  
• Version 1.1: 2024-05-01
  Changes: Data collection, Refinement description
• Version 1.2: 2024-10-09
  Changes: Structure summary