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- PDB-6sot: Fragment N11290a in complex with MAP kinase p38-alpha -

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Basic information

Entry
Database: PDB / ID: 6sot
TitleFragment N11290a in complex with MAP kinase p38-alpha
ComponentsMitogen-activated protein kinase 14MAPK14
KeywordsTRANSFERASE / FBDD / Fragment Based Drug Design / P38 / MAPK14 / Kinase / Transferase.
Function / homology
Function and homology information


DSCAM interactions / p38MAPK events / Activation of the AP-1 family of transcription factors / Platelet sensitization by LDL / RHO GTPases Activate NADPH Oxidases / ERK/MAPK targets / activated TAK1 mediates p38 MAPK activation / NOD1/2 Signaling Pathway / ADP signalling through P2Y purinoceptor 1 / Oxidative Stress Induced Senescence ...DSCAM interactions / p38MAPK events / Activation of the AP-1 family of transcription factors / Platelet sensitization by LDL / RHO GTPases Activate NADPH Oxidases / ERK/MAPK targets / activated TAK1 mediates p38 MAPK activation / NOD1/2 Signaling Pathway / ADP signalling through P2Y purinoceptor 1 / Oxidative Stress Induced Senescence / Regulation of TP53 Activity through Phosphorylation / Myogenesis / VEGFA-VEGFR2 Pathway / regulation of synaptic membrane adhesion / stress-induced premature senescence / cell surface receptor protein serine/threonine kinase signaling pathway / cartilage condensation / cellular response to UV-B / stress-activated protein kinase signaling cascade / mitogen-activated protein kinase p38 binding / positive regulation of myoblast fusion / negative regulation of hippo signaling / positive regulation of myotube differentiation / NFAT protein binding / glucose import / regulation of cytokine production involved in inflammatory response / p38MAPK cascade / fatty acid oxidation / cellular response to lipoteichoic acid / response to dietary excess / response to muramyl dipeptide / regulation of ossification / MAP kinase activity / mitogen-activated protein kinase / cellular response to vascular endothelial growth factor stimulus / positive regulation of myoblast differentiation / chondrocyte differentiation / vascular endothelial growth factor receptor signaling pathway / stress-activated MAPK cascade / signal transduction in response to DNA damage / skeletal muscle tissue development / lipopolysaccharide-mediated signaling pathway / positive regulation of cardiac muscle cell proliferation / striated muscle cell differentiation / response to muscle stretch / Neutrophil degranulation / positive regulation of brown fat cell differentiation / positive regulation of interleukin-12 production / osteoclast differentiation / positive regulation of erythrocyte differentiation / placenta development / DNA damage checkpoint signaling / cellular response to ionizing radiation / stem cell differentiation / positive regulation of glucose import / response to insulin / bone development / cell morphogenesis / negative regulation of canonical Wnt signaling pathway / cellular response to virus / osteoblast differentiation / spindle pole / positive regulation of protein import into nucleus / glucose metabolic process / positive regulation of reactive oxygen species metabolic process / MAPK cascade / cellular response to tumor necrosis factor / kinase activity / peptidyl-serine phosphorylation / protein phosphatase binding / angiogenesis / cellular response to lipopolysaccharide / response to lipopolysaccharide / transcription by RNA polymerase II / protein kinase activity / intracellular signal transduction / nuclear speck / protein serine kinase activity / protein serine/threonine kinase activity / glutamatergic synapse / apoptotic process / DNA damage response / positive regulation of gene expression / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / enzyme binding / positive regulation of transcription by RNA polymerase II / mitochondrion / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Mitogen-activated protein kinase 14 / Mitogen-activated protein (MAP) kinase p38-like / Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. / 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
Similarity search - Domain/homology
1-(4-methylphenyl)pyrrolidine-2,5-dione / Mitogen-activated protein kinase 14
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 Å
AuthorsNichols, C.E. / De Nicola, G.F.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
British Heart FoundationSP/14/2/30922 United Kingdom
CitationJournal: J.Med.Chem. / Year: 2020
Title: Mining the PDB for Tractable Cases Where X-ray Crystallography Combined with Fragment Screens Can Be Used to Systematically Design Protein-Protein Inhibitors: Two Test Cases Illustrated by IL1 ...Title: Mining the PDB for Tractable Cases Where X-ray Crystallography Combined with Fragment Screens Can Be Used to Systematically Design Protein-Protein Inhibitors: Two Test Cases Illustrated by IL1 beta-IL1R and p38 alpha-TAB1 Complexes.
Authors: Nichols, C. / Ng, J. / Keshu, A. / Kelly, G. / Conte, M.R. / Marber, M.S. / Fraternali, F. / De Nicola, G.F.
History
DepositionAug 29, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 2, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2020Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_struct_conn_angle / struct_conn
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Mitogen-activated protein kinase 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,51612
Polymers43,8091
Non-polymers70711
Water4,954275
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1600 Å2
ΔGint-79 kcal/mol
Surface area16690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.001, 85.815, 127.218
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Mitogen-activated protein kinase 14 / MAPK14 / MAPK 14 / CRK1 / Mitogen-activated protein kinase p38 alpha / MAP kinase p38 alpha


Mass: 43808.738 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Mapk14, Crk1, Csbp1, Csbp2 / Production host: Escherichia coli (E. coli)
References: UniProt: P47811, mitogen-activated protein kinase

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Non-polymers , 6 types, 286 molecules

#2: Chemical ChemComp-LOQ / 1-(4-methylphenyl)pyrrolidine-2,5-dione


Mass: 189.211 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H11NO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 275 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 3.19 Å3/Da / Density % sol: 61.49 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 27.5% PEG3350, 0.1M magnesium chloride, 0.1M magnesium sulphate, 0.1M bis-tris propane, 10% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.54→85.81 Å / Num. obs: 75111 / % possible obs: 99.7 % / Redundancy: 6.3 % / Biso Wilson estimate: 19.12 Å2 / CC1/2: 0.999 / Net I/σ(I): 11.3
Reflection shellResolution: 1.54→1.58 Å / Redundancy: 5.4 % / Mean I/σ(I) obs: 1 / Num. unique obs: 5444 / CC1/2: 0.525 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
PHENIX1.16_3549refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6SO1

6so1


Resolution: 1.54→71.14 Å / SU ML: 0.2412 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 26.1826
RfactorNum. reflection% reflection
Rfree0.2312 7117 4.96 %
Rwork0.2097 --
obs0.2108 75019 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 25.11 Å2
Refinement stepCycle: LAST / Resolution: 1.54→71.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2696 0 38 275 3009
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00812803
X-RAY DIFFRACTIONf_angle_d0.75923813
X-RAY DIFFRACTIONf_chiral_restr0.0514430
X-RAY DIFFRACTIONf_plane_restr0.0055496
X-RAY DIFFRACTIONf_dihedral_angle_d2.25262300
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.54-1.560.38522310.36964477X-RAY DIFFRACTION99.37
1.56-1.580.36762620.35734534X-RAY DIFFRACTION99.83
1.58-1.60.36262440.35034549X-RAY DIFFRACTION98.89
1.6-1.620.37792350.34064498X-RAY DIFFRACTION99.81
1.62-1.640.32622270.32714563X-RAY DIFFRACTION99.77
1.64-1.660.32722370.32084559X-RAY DIFFRACTION99.81
1.66-1.680.33962290.31844544X-RAY DIFFRACTION99.54
1.68-1.710.3552490.30964623X-RAY DIFFRACTION99.69
1.71-1.730.27732160.32094474X-RAY DIFFRACTION99.49
1.73-1.760.3552710.30654587X-RAY DIFFRACTION99.67
1.76-1.790.29532160.29024496X-RAY DIFFRACTION99.58
1.79-1.830.32542640.28014550X-RAY DIFFRACTION99.67
1.83-1.860.28522700.26264472X-RAY DIFFRACTION99.77
1.86-1.90.28792400.24654539X-RAY DIFFRACTION99.38
1.9-1.940.23132550.23574529X-RAY DIFFRACTION99.9
1.94-1.990.25732460.22124592X-RAY DIFFRACTION99.71
1.99-2.040.22852190.224517X-RAY DIFFRACTION99.58
2.04-2.090.25362590.21824549X-RAY DIFFRACTION99.65
2.09-2.150.22962130.20214533X-RAY DIFFRACTION99.54
2.15-2.220.2132150.18874571X-RAY DIFFRACTION99.48
2.22-2.30.24212150.19884581X-RAY DIFFRACTION99.65
2.3-2.390.21852340.19974560X-RAY DIFFRACTION99.79
2.39-2.50.2322350.19164542X-RAY DIFFRACTION99.71
2.5-2.630.24112440.1984549X-RAY DIFFRACTION99.96
2.63-2.80.21122520.19724530X-RAY DIFFRACTION99.94
2.8-3.010.25391830.19924614X-RAY DIFFRACTION99.77
3.01-3.320.21612470.19364536X-RAY DIFFRACTION99.34
3.32-3.80.21032100.17234551X-RAY DIFFRACTION99.25
3.8-4.780.16342650.15544533X-RAY DIFFRACTION100
4.78-71.140.16372340.17964526X-RAY DIFFRACTION99.21

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