8A66 | pdb_00008a66

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 (Depositor), 0.254 (DCC)
R-Value Work:
0.218 (Depositor), 0.212 (DCC)
R-Value Observed:
0.220 (Depositor)

Starting Model: other
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.2 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., Nawrotek, A.

To be published.

Macromolecule Content

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

Macromolecules

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| 3D Structure

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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q13188
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q13188
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 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 F [auth B] SDF format, chain C [auth A] MOL2 format, chain F [auth B] MOL2 format, chain C [auth A] mmCIF format, chain F [auth B] mmCIF format, chain C [auth A]	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		Interactions Focus chain C [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A], E [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A]

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

Binding Affinity Annotations
ID	Source	Binding Affinity
5BS	BindingDB: 8A66	Kd: min: 11, max: 17 (nM) from 2 assay(s)
5BS	BindingDB: 8A66	IC50: min: 9.8, max: 4036 (nM) from 21 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.258 (Depositor), 0.254 (DCC)
R-Value Work: 0.218 (Depositor), 0.212 (DCC)
R-Value Observed: 0.220 (Depositor)

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

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2022-07-20

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

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