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- PDB-4zsg: MITOGEN ACTIVATED PROTEIN KINASE 7 IN COMPLEX WITH INHIBITOR -

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Basic information

Entry
Database: PDB / ID: 4zsg
TitleMITOGEN ACTIVATED PROTEIN KINASE 7 IN COMPLEX WITH INHIBITOR
ComponentsMitogen-activated protein kinase 7
KeywordsKINASE / INHIBITOR
Function / homology
Function and homology information


Signalling to ERK5 / negative regulation of response to cytokine stimulus / negative regulation of heterotypic cell-cell adhesion / calcineurin-NFAT signaling cascade / cellular response to laminar fluid shear stress / Gastrin-CREB signalling pathway via PKC and MAPK / ERKs are inactivated / enzyme inhibitor activity / mitogen-activated protein kinase binding / negative regulation of calcineurin-NFAT signaling cascade ...Signalling to ERK5 / negative regulation of response to cytokine stimulus / negative regulation of heterotypic cell-cell adhesion / calcineurin-NFAT signaling cascade / cellular response to laminar fluid shear stress / Gastrin-CREB signalling pathway via PKC and MAPK / ERKs are inactivated / enzyme inhibitor activity / mitogen-activated protein kinase binding / negative regulation of calcineurin-NFAT signaling cascade / ERK/MAPK targets / negative regulation of smooth muscle cell apoptotic process / RET signaling / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / MAP kinase activity / mitogen-activated protein kinase / regulation of angiogenesis / negative regulation of endothelial cell apoptotic process / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / cellular response to transforming growth factor beta stimulus / positive regulation of protein metabolic process / adenylate cyclase-activating G protein-coupled receptor signaling pathway / cellular response to growth factor stimulus / PML body / negative regulation of inflammatory response / cellular response to hydrogen peroxide / MAPK cascade / Senescence-Associated Secretory Phenotype (SASP) / cell differentiation / intracellular signal transduction / protein serine kinase activity / protein serine/threonine kinase activity / signal transduction / positive regulation of transcription by RNA polymerase II / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. / : / 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 ...Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. / : / 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-4QX / Mitogen-activated protein kinase 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å
AuthorsTucker, J. / Ogg, D.J.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2016
Title: Discovery of a novel allosteric inhibitor-binding site in ERK5: comparison with the canonical kinase hinge ATP-binding site.
Authors: Chen, H. / Tucker, J. / Wang, X. / Gavine, P.R. / Phillips, C. / Augustin, M.A. / Schreiner, P. / Steinbacher, S. / Preston, M. / Ogg, D.
History
DepositionMay 13, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 4, 2016Provider: repository / Type: Initial release
Revision 1.1May 11, 2016Group: Database references
Revision 1.2May 1, 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 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,5117
Polymers39,7561
Non-polymers7556
Water6,197344
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1010 Å2
ΔGint2 kcal/mol
Surface area15930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.530, 92.530, 107.480
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-598-

HOH

21A-839-

HOH

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Components

#1: Protein Mitogen-activated protein kinase 7 / MAPK 7 / Big MAP kinase 1 / BMK-1 / Extracellular signal-regulated kinase 5 / ERK-5


Mass: 39755.777 Da / Num. of mol.: 1 / Fragment: residues 47-393
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAPK7, BMK1, ERK5, PRKM7 / Plasmid: pFastBac HT A / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q13164, mitogen-activated protein kinase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-4QX / 3-amino-5-[(4-chlorophenyl)amino]-N-(propan-2-yl)-1H-1,2,4-triazole-1-carboxamide


Mass: 294.740 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H15ClN6O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 344 / 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: 2.89 Å3/Da / Density % sol: 57.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.25 / Details: 4-6 % w/v PEG 6000, 0.1 M MES, 5 mM DTT / PH range: 6.25

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.972 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 22, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972 Å / Relative weight: 1
ReflectionResolution: 1.79→50 Å / Num. obs: 44410 / % possible obs: 99.4 % / Redundancy: 10.6 % / Biso Wilson estimate: 35.39 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 20.9
Reflection shellResolution: 1.79→1.85 Å / Redundancy: 10.8 % / Mean I/σ(I) obs: 1.7 / % possible all: 98.7

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Processing

Software
NameClassification
XDSdata reduction
SCALAdata scaling
BUSTERrefinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: unpublished in-house Erk5/MAPK7 structure

Resolution: 1.79→50 Å / SU R Cruickshank DPI: 0.117 / Cross valid method: FREE R-VALUE / SU R Blow DPI: 0.125 / SU Rfree Blow DPI: 0.118 / SU Rfree Cruickshank DPI: 0.114
RfactorNum. reflection% reflectionSelection details
Rfree0.2352 2208 5 %Random selection
Rwork0.2041 ---
obs0.2057 43910 99.4 %-
Displacement parametersBiso mean: 55.62 Å2
Baniso -1Baniso -2Baniso -3
1--2.2812 Å20 Å20 Å2
2---2.2812 Å20 Å2
3---4.5625 Å2
Refine analyzeLuzzati coordinate error obs: 0.516 Å
Refinement stepCycle: LAST / Resolution: 1.79→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2772 0 50 344 3166
LS refinement shellResolution: 1.79→1.85 Å
RfactorNum. reflection% reflection
Rfree0.2276 144 4.5 %
Rwork0.2198 3199 -
obs--98.5 %
Refinement TLS params.Method: refined / Details: Chain A catalytic domain / Origin x: 9.3624 Å / Origin y: -32.9683 Å / Origin z: -3.8049 Å
111213212223313233
T-0.0989 Å2-0.1572 Å2-0.0117 Å2--0.0542 Å2-0.0986 Å2---0.4225 Å2
L1.5827 °20.1359 °2-0.6286 °2-0.7605 °20.2173 °2--3.883 °2
S0.2732 Å °-0.24 Å °0.1301 Å °-0.2274 Å °0.5983 Å °-0.0471 Å °0.1064 Å °-0.2261 Å °-0.0027 Å °
Refinement TLS groupSelection: all

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