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- PDB-7nrb: Re-refinement of MK3-inhibitor complex -

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Basic information

Entry
Database: PDB / ID: 7nrb
TitleRe-refinement of MK3-inhibitor complex
ComponentsMAP kinase-activated protein kinase 3
KeywordsTRANSFERASE / kinase
Function / homology
Function and homology information


macropinocytosis / calcium-dependent protein serine/threonine kinase activity / calmodulin-dependent protein kinase activity / mitogen-activated protein kinase binding / toll-like receptor signaling pathway / MAP kinase kinase activity / vascular endothelial growth factor receptor signaling pathway / p38MAPK events / response to cytokine / activated TAK1 mediates p38 MAPK activation ...macropinocytosis / calcium-dependent protein serine/threonine kinase activity / calmodulin-dependent protein kinase activity / mitogen-activated protein kinase binding / toll-like receptor signaling pathway / MAP kinase kinase activity / vascular endothelial growth factor receptor signaling pathway / p38MAPK events / response to cytokine / activated TAK1 mediates p38 MAPK activation / VEGFA-VEGFR2 Pathway / peptidyl-serine phosphorylation / Oxidative Stress Induced Senescence / response to lipopolysaccharide / calmodulin binding / non-specific serine/threonine protein kinase / intracellular signal transduction / protein serine kinase activity / protein serine/threonine kinase activity / signal transduction / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
MAP kinase activated protein kinase, C-terminal / 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
Similarity search - Domain/homology
Chem-P4O / MAP kinase-activated protein kinase 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsCroll, T.I. / Read, R.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust209407/Z/17/Z United Kingdom
Citation
Journal: Acta Crystallogr D Struct Biol / Year: 2021
Title: Adaptive Cartesian and torsional restraints for interactive model rebuilding.
Authors: Croll, T.I. / Read, R.J.
#1: Journal: Acta Crystallogr D Struct Biol / Year: 2018
Title: ISOLDE: a physically realistic environment for model building into low-resolution electron-density maps.
Authors: Croll, T.I.
History
DepositionMar 3, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 12, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MAP kinase-activated protein kinase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9152
Polymers38,5751
Non-polymers3401
Water2,522140
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area770 Å2
ΔGint5 kcal/mol
Surface area13210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.688, 74.832, 60.664
Angle α, β, γ (deg.)90.000, 107.340, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein MAP kinase-activated protein kinase 3 / MAPK-activated protein kinase 3 / MAPKAP kinase 3 / MAPKAP-K3 / MAPKAPK-3 / MK-3 / Chromosome 3p kinase / 3pK


Mass: 38574.980 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAPKAPK3 / Production host: Escherichia coli (E. coli)
References: UniProt: Q16644, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-P4O / 2-(2-QUINOLIN-3-YLPYRIDIN-4-YL)-1,5,6,7-TETRAHYDRO-4H-PYRROLO[3,2-C]PYRIDIN-4-ONE


Mass: 340.378 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H16N4O
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 140 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.38 Å3/Da / Density % sol: 48.28 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop
Details: 10%-15% PEG 3350, 100mM BisTris propane/citric acid, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9769 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 30, 2008
RadiationMonochromator: double Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9769 Å / Relative weight: 1
ReflectionResolution: 1.9→31.43 Å / Num. obs: 27952 / % possible obs: 97.9 % / Redundancy: 3.37 % / Biso Wilson estimate: 38.25 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 10.3
Reflection shellResolution: 1.9→1.97 Å / Rmerge(I) obs: 0.451 / Num. unique obs: 2500

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Processing

Software
NameVersionClassification
ISOLDE1.1.0refinement
PHENIXdev_3964refinement
CrystalCleardata reduction
CrystalCleardata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3fhr

3fhr


Resolution: 1.9→27.78 Å / SU ML: 0.3909 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.7404
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2355 1422 5.09 %
Rwork0.2124 26516 -
obs0.2137 27938 97.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.59 Å2
Refinement stepCycle: LAST / Resolution: 1.9→27.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2213 0 26 140 2379
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00282301
X-RAY DIFFRACTIONf_angle_d0.6543112
X-RAY DIFFRACTIONf_chiral_restr0.0419335
X-RAY DIFFRACTIONf_plane_restr0.0048399
X-RAY DIFFRACTIONf_dihedral_angle_d13.8477862
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.970.49531010.46422325X-RAY DIFFRACTION84.97
1.97-2.050.42011470.3872571X-RAY DIFFRACTION96.76
2.05-2.140.36161460.33052706X-RAY DIFFRACTION99.86
2.14-2.250.34221260.27652714X-RAY DIFFRACTION99.93
2.25-2.390.23851570.24132663X-RAY DIFFRACTION99.89
2.39-2.580.29531480.2372714X-RAY DIFFRACTION99.83
2.58-2.840.26441350.22812715X-RAY DIFFRACTION99.86
2.84-3.250.22691480.20642699X-RAY DIFFRACTION99.79
3.25-4.090.19171530.17782700X-RAY DIFFRACTION99.51
4.09-27.780.2031610.17072709X-RAY DIFFRACTION98.25

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