8A66

Crystal structure of MST2 in complex with XMU-MP-1

• PDB DOI: https://doi.org/10.2210/pdb8A66/pdb

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


• Deposited: 2022-06-16 Released: 2022-07-20 
• Deposition Author(s): Nawrotek, A., Vuillard, L., Miallau, L., Weber, C.
• Funding Organization(s): Not funded

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.258 
• R-Value Work: 0.218 
• R-Value Observed: 0.220 

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., Nawrotek, A.

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: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 68.89 kDa 
• Atom Count: 4,757 
• Modelled Residue Count: 557 
• Deposited Residue Count: 596 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein kinase 3 36kDa subunit	A	298	Homo sapiens	Mutation(s): 0  Gene Names: STK3, KRS1, MST2 EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q13188 (Homo sapiens) Explore Q13188  Go to UniProtKB:  Q13188
PHAROS:  Q13188 GTEx:  ENSG00000104375

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein kinase 3 36kDa subunit	B	298	Homo sapiens	Mutation(s): 0  Gene Names: STK3, KRS1, MST2 EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q13188 (Homo sapiens) Explore Q13188  Go to UniProtKB:  Q13188
PHAROS:  Q13188 GTEx:  ENSG00000104375

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
5BS (Subject of Investigation/LOI)	C [auth A], F [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
NA	D [auth A], E [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

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

Binding Affinity Annotations
ID	Source	Binding Affinity
5BS	BindingDB:  8A66	IC50: min: 104, max: 1510 (nM) from 3 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.258 
• R-Value Work: 0.218 
• R-Value Observed: 0.220 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.77	α = 90
b = 99.04	β = 90
c = 167.29	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: 2022-07-20 
Deposition Author(s): Nawrotek, A., Vuillard, L., Miallau, L., Weber, C.

---

Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2022-07-20
  Type: Initial release
  
• Version 2.0: 2022-12-07
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Other, Polymer sequence, Source and taxonomy, Structure summary
• Version 2.1: 2024-05-01
  Changes: Data collection, Refinement description
• Version 2.2: 2024-10-23
  Changes: Structure summary