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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.12 Å
R-Value Free:
0.248 (Depositor), 0.244 (DCC)
R-Value Work:
0.243 (Depositor), 0.232 (DCC)
R-Value Observed:
0.243 (Depositor)

Starting Model: other
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Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

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.

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

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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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q13043
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
5BS (Subject of Investigation/LOI) Query on 5BS Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	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		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

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

Binding Affinity Annotations
ID	Source	Binding Affinity
5BS	BindingDB: 8A5J	Kd: min: 11, max: 17 (nM) from 2 assay(s)
5BS	BindingDB: 8A5J	IC50: min: 9.8, max: 4036 (nM) from 21 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.12 Å
R-Value Free: 0.248 (Depositor), 0.244 (DCC)
R-Value Work: 0.243 (Depositor), 0.232 (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

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2022-07-13

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.