[English] 日本語
Yorodumi
- PDB-4qmm: MST3 IN COMPLEX WITH AT-9283, 4-[(2-{4-[(CYCLOPROPYLCARBAMOYL)AMI... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4qmm
TitleMST3 IN COMPLEX WITH AT-9283, 4-[(2-{4-[(CYCLOPROPYLCARBAMOYL)AMINO]-1H-PYRAZOL-3-YL}-1H-BENZIMIDAZOL-6-YL)METHYL]MORPHOLIN-4-IUM
ComponentsSerine/threonine-protein kinase 24
KeywordsTransferase/transferase inhibitor / PROTEIN KINASE / MST3 / STK24 / STERILE 20-LIKE KINASE / ATP-BINDING / NUCLEOTIDE-BINDING / PHOSPHOPROTEIN / SERINE/THREONINE-TRANSFERASE / Transferase-transferase inhibitor complex
Function / homology
Function and homology information


Apoptotic execution phase / FAR/SIN/STRIPAK complex / regulation of axon regeneration / intrinsic apoptotic signaling pathway in response to oxidative stress / execution phase of apoptosis / Apoptotic cleavage of cellular proteins / negative regulation of cell migration / cellular response to starvation / protein autophosphorylation / cellular response to oxidative stress ...Apoptotic execution phase / FAR/SIN/STRIPAK complex / regulation of axon regeneration / intrinsic apoptotic signaling pathway in response to oxidative stress / execution phase of apoptosis / Apoptotic cleavage of cellular proteins / negative regulation of cell migration / cellular response to starvation / protein autophosphorylation / cellular response to oxidative stress / protein phosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / cadherin binding / protein serine kinase activity / protein serine/threonine kinase activity / nucleolus / Golgi apparatus / signal transduction / extracellular exosome / nucleoplasm / ATP binding / metal ion binding / nucleus / membrane / cytoplasm / cytosol
Similarity search - Function
Programmed cell death protein 10, dimerisation domain superfamily / : / Programmed cell death protein 10, dimerisation domain / : / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain ...Programmed cell death protein 10, dimerisation domain superfamily / : / Programmed cell death protein 10, dimerisation domain / : / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-35R / ACETATE ION / Serine/threonine-protein kinase 24
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.852 Å
AuthorsOlesen, S.H. / Watts, C. / Zhu, J.-Y. / Schonbrunn, E.
CitationJournal: Chemmedchem / Year: 2016
Title: Discovery of Diverse Small-Molecule Inhibitors of Mammalian Sterile20-like Kinase 3 (MST3).
Authors: Olesen, S.H. / Zhu, J.Y. / Martin, M.P. / Schonbrunn, E.
History
DepositionJun 16, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 15, 2016Group: Database references
Revision 1.2Jul 13, 2016Group: Database references
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Serine/threonine-protein kinase 24
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6837
Polymers35,0241
Non-polymers6596
Water3,351186
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)99.653, 58.636, 61.789
Angle α, β, γ (deg.)90.00, 94.11, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-685-

HOH

Detailsmonomer per ASU

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Serine/threonine-protein kinase 24 / Mammalian STE20-like protein kinase 3 / MST-3 / STE20-like kinase MST3 / Serine/threonine-protein ...Mammalian STE20-like protein kinase 3 / MST-3 / STE20-like kinase MST3 / Serine/threonine-protein kinase 24 36 kDa subunit / Mammalian STE20-like protein kinase 3 N-terminal / MST3/N / Serine/threonine-protein kinase 24 12 kDa subunit / Mammalian STE20-like protein kinase 3 C-terminal / MST3/C


Mass: 35023.934 Da / Num. of mol.: 1 / Fragment: unp residues 1-303
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MST3, STK24, STK3 / Plasmid: PET28A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) RIL
References: UniProt: Q9Y6E0, non-specific serine/threonine protein kinase

-
Non-polymers , 5 types, 192 molecules

#2: Chemical ChemComp-35R / 1-cyclopropyl-3-{3-[5-(morpholin-4-ylmethyl)-1H-benzimidazol-2-yl]-1H-pyrazol-4-yl}urea


Mass: 381.432 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H23N7O2
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 186 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY
Sequence detailsTHE CRYSTALLIZED SEQUENCE REFERS TO THE ISOFORM A

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.57 Å3/Da / Density % sol: 52.15 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 12.5 mg/mL MST3, 1 mM AT-9283, 25 mM TRIS, 50 MM HEPES pH 7.5, 125 mM SODIUM CHLORIDE, 100 mM MAGNESIUM CHLORIDE, 15% PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 19, 2014
RadiationMonochromator: ROSENBAUM-ROCK DOUBLE-CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→20 Å / Num. obs: 29959 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Rsym value: 0.035 / Net I/σ(I): 41.9
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 4.58 / Rsym value: 0.188 / % possible all: 87.5

-
Processing

Software
NameVersionClassification
SERGUIdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.8.4_1496)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3CKW

3ckw


Resolution: 1.852→19.89 Å / SU ML: 0.16 / σ(F): 1.37 / Phase error: 19.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1981 1996 6.66 %
Rwork0.1413 --
obs-29954 98.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.852→19.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2310 0 45 186 2541
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062403
X-RAY DIFFRACTIONf_angle_d1.0213244
X-RAY DIFFRACTIONf_dihedral_angle_d15.007928
X-RAY DIFFRACTIONf_chiral_restr0.038356
X-RAY DIFFRACTIONf_plane_restr0.005410
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8516-1.89790.24771160.14821715X-RAY DIFFRACTION86
1.8979-1.94910.24551290.1481967X-RAY DIFFRACTION97
1.9491-2.00640.23261540.1352011X-RAY DIFFRACTION100
2.0064-2.07110.22521510.1332005X-RAY DIFFRACTION100
2.0711-2.14510.20761500.13122013X-RAY DIFFRACTION100
2.1451-2.23080.21271500.13131990X-RAY DIFFRACTION100
2.2308-2.33220.22021340.12952019X-RAY DIFFRACTION100
2.3322-2.4550.19621400.13842015X-RAY DIFFRACTION100
2.455-2.60850.21861430.14412022X-RAY DIFFRACTION100
2.6085-2.80940.22831380.16732044X-RAY DIFFRACTION100
2.8094-3.09110.21211470.1712022X-RAY DIFFRACTION100
3.0911-3.53630.19421470.15832022X-RAY DIFFRACTION100
3.5363-4.44710.15791500.12672046X-RAY DIFFRACTION100
4.4471-19.89070.17731470.12492067X-RAY DIFFRACTION99

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more