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- PDB-4rvt: MAP4K4 in complex with a pyridin-2(1H)-one derivative -

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Basic information

Entry
Database: PDB / ID: 4rvt
TitleMAP4K4 in complex with a pyridin-2(1H)-one derivative
ComponentsMitogen-activated protein kinase kinase kinase kinase 4
KeywordsTransferase/Transferase inhibitor / Pyridin-2(1H)-one Ligand / Type I / DFG-in / Serine/Threonine kinase / Transferase-Transferase inhibitor complex
Function / homology
Function and homology information


positive regulation of ARF protein signal transduction / creatine kinase activity / positive regulation of keratinocyte migration / positive regulation of focal adhesion disassembly / negative regulation of cell-matrix adhesion / positive regulation of focal adhesion assembly / regulation of MAPK cascade / regulation of JNK cascade / neuron projection morphogenesis / positive regulation of GTPase activity ...positive regulation of ARF protein signal transduction / creatine kinase activity / positive regulation of keratinocyte migration / positive regulation of focal adhesion disassembly / negative regulation of cell-matrix adhesion / positive regulation of focal adhesion assembly / regulation of MAPK cascade / regulation of JNK cascade / neuron projection morphogenesis / positive regulation of GTPase activity / MAPK cascade / microtubule binding / Oxidative Stress Induced Senescence / non-specific serine/threonine protein kinase / positive regulation of cell migration / intracellular signal transduction / protein phosphorylation / focal adhesion / protein serine kinase activity / protein serine/threonine kinase activity / negative regulation of apoptotic process / ATP binding / cytoplasm
Similarity search - Function
Domain found in NIK1-like kinases, mouse citron and yeast ROM1, ROM2 / Citron homology (CNH) domain / CNH domain / Citron homology (CNH) domain profile. / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. ...Domain found in NIK1-like kinases, mouse citron and yeast ROM1, ROM2 / Citron homology (CNH) domain / CNH domain / Citron homology (CNH) domain profile. / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site 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 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-3XM / Mitogen-activated protein kinase kinase kinase kinase 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsRichters, A. / Becker, C. / Kleine, S. / Rauh, D.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2015
Title: Neuritogenic Militarinone-Inspired 4-Hydroxypyridones Target the Stress Pathway Kinase MAP4K4.
Authors: Schroder, P. / Forster, T. / Kleine, S. / Becker, C. / Richters, A. / Ziegler, S. / Rauh, D. / Kumar, K. / Waldmann, H.
History
DepositionNov 27, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 27, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2015Group: Database references / Other
Revision 1.2Sep 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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Mitogen-activated protein kinase kinase kinase kinase 4
B: Mitogen-activated protein kinase kinase kinase kinase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,5684
Polymers75,0722
Non-polymers4972
Water1,36976
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3570 Å2
ΔGint-18 kcal/mol
Surface area26530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.990, 90.250, 90.970
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Mitogen-activated protein kinase kinase kinase kinase 4 / HPK/GCK-like kinase HGK / MAPK/ERK kinase kinase kinase 4 / MEK kinase kinase 4 / MEKKK 4 / Nck- ...HPK/GCK-like kinase HGK / MAPK/ERK kinase kinase kinase 4 / MEK kinase kinase 4 / MEKKK 4 / Nck-interacting kinase


Mass: 37535.883 Da / Num. of mol.: 2 / Fragment: kinase domain (UNP residues 1-325)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HGK, KIAA0687, MAP4K4, NIK / Plasmid: pIEx/Bac3 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: O95819, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-3XM / 3-hexanoyl-4-hydroxy-5-(4-hydroxyphenyl)pyridin-2(1H)-one


Mass: 301.337 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H19NO4
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 76 / Source method: isolated from a natural source / Formula: H2O

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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: 2.19 Å3/Da / Density % sol: 43.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: 0.1M MES, 14% v/v PEG 8000, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.00718 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 29, 2014 / Details: Dynamic bendable mirror
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00718 Å / Relative weight: 1
ReflectionResolution: 2.4→45.49 Å / Num. all: 26397 / Num. obs: 26382 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 6.47 % / Biso Wilson estimate: 58.827 Å2 / Rmerge(I) obs: 0.089 / Χ2: 0.997 / Net I/σ(I): 16.64
Reflection shell

Rmerge(I) obs: 0.012 / Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured obsNum. unique allNum. unique obs% possible all
2.4-2.466.81.791310019261926100
2.46-2.532.1812643187599.9
2.53-2.62.8112046181299.9
2.6-2.683.69114351772100
2.68-2.774.4410569171199.9
2.77-2.875.63105241671100
2.87-2.987.93108711608100
2.98-3.19.83105301549100
3.1-3.2412.44100171491100
3.24-3.3916.4193821419100
3.39-3.5820.5885061367100
3.58-3.7926.1379711305100
3.79-4.0631.6680021206100
4.06-4.3836.4674931140100
4.38-4.839.756712105499.9
4.8-5.3737.66563396599.7
5.37-6.238.27525784499.8
6.2-7.5943.384764747100
7.59-10.7350.77325757499.8
10.7355.06189834698.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.82 Å45.48 Å
Translation5.82 Å45.48 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.5.5phasing
REFMAC5.8.0049refinement
PDB_EXTRACT3.15data extraction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 4U43

4u43


Resolution: 2.4→45.49 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.91 / WRfactor Rfree: 0.2621 / WRfactor Rwork: 0.1905 / FOM work R set: 0.7698 / SU B: 10.405 / SU ML: 0.236 / SU R Cruickshank DPI: 0.4443 / SU Rfree: 0.2939 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.444 / ESU R Free: 0.294 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2776 1319 5 %RANDOM
Rwork0.2087 ---
obs0.2121 26382 99.93 %-
all-26397 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 138.85 Å2 / Biso mean: 54.233 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1--0.98 Å20 Å2-0 Å2
2--1.26 Å2-0 Å2
3----0.28 Å2
Refinement stepCycle: LAST / Resolution: 2.4→45.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4585 0 34 76 4695
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0194750
X-RAY DIFFRACTIONr_angle_refined_deg1.2251.9636442
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8725577
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.14823.981216
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.99815811
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4531529
X-RAY DIFFRACTIONr_chiral_restr0.0910.2706
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213595
X-RAY DIFFRACTIONr_mcbond_it2.5615.4012317
X-RAY DIFFRACTIONr_mcangle_it4.1218.082891
X-RAY DIFFRACTIONr_scbond_it2.875.5772433
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.377 96 -
Rwork0.323 1825 -
all-1921 -
obs-1926 99.9 %

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