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- PDB-6yky: Biochemical, Cellular and Structural Characterization of Novel ER... -

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Basic information

Entry
Database: PDB / ID: 6yky
TitleBiochemical, Cellular and Structural Characterization of Novel ERK3 Inhibitors
ComponentsMitogen-activated protein kinase 6
KeywordsTRANSFERASE / Mitogen-activated protein kinase 6
Function / homology
Function and homology information


septin cytoskeleton / positive regulation of dendritic spine development / MAP kinase activity / mitogen-activated protein kinase / MAPK6/MAPK4 signaling / protein phosphorylation / intracellular signal transduction / protein heterodimerization activity / protein serine kinase activity / protein serine/threonine kinase activity ...septin cytoskeleton / positive regulation of dendritic spine development / MAP kinase activity / mitogen-activated protein kinase / MAPK6/MAPK4 signaling / protein phosphorylation / intracellular signal transduction / protein heterodimerization activity / protein serine kinase activity / protein serine/threonine kinase activity / protein kinase binding / signal transduction / protein-containing complex / nucleoplasm / ATP binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Mitogen-activated protein (MAP) kinase, ERK3/4 / : / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain ...Mitogen-activated protein (MAP) kinase, ERK3/4 / : / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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-OWQ / Mitogen-activated protein kinase 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.52 Å
AuthorsGraedler, U.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2020
Title: Biochemical, cellular and structural characterization of novel and selective ERK3 inhibitors.
Authors: Gradler, U. / Busch, M. / Leuthner, B. / Raba, M. / Burgdorf, L. / Lehmann, M. / Linde, N. / Esdar, C.
History
DepositionApr 6, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 23, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 30, 2020Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
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 6
B: Mitogen-activated protein kinase 6
C: Mitogen-activated protein kinase 6
D: Mitogen-activated protein kinase 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,3288
Polymers144,7754
Non-polymers1,5544
Water3,405189
1
A: Mitogen-activated protein kinase 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,5822
Polymers36,1941
Non-polymers3881
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Mitogen-activated protein kinase 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,5822
Polymers36,1941
Non-polymers3881
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Mitogen-activated protein kinase 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,5822
Polymers36,1941
Non-polymers3881
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Mitogen-activated protein kinase 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,5822
Polymers36,1941
Non-polymers3881
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.978, 100.883, 195.522
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 6 / MAPK 6 / Extracellular signal-regulated kinase 3 / ERK-3 / MAP kinase isoform p97 / p97-MAPK


Mass: 36193.672 Da / Num. of mol.: 4 / Mutation: L290V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAPK6, ERK3, PRKM6 / Production host: Escherichia coli (E. coli)
References: UniProt: Q16659, mitogen-activated protein kinase
#2: Chemical
ChemComp-OWQ / 3-(4-methoxyphenyl)-~{N}-[(3~{R})-1-pyridin-4-ylpyrrolidin-3-yl]-[1,2,3]triazolo[4,5-d]pyrimidin-5-amine


Mass: 388.426 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C20H20N8O / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 189 / Source method: isolated from a natural source / Formula: H2O
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: 2.49 Å3/Da / Density % sol: 50.67 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 100 mM Bis-Tris (pH 6), 100 mM Lithium acetate, 18%v/v Sokalan CP42, 3%vv Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 25, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 2.52→65.9 Å / Num. obs: 36937 / % possible obs: 92.8 % / Redundancy: 4.1 % / Biso Wilson estimate: 74.12 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.051 / Rrim(I) all: 0.109 / Rsym value: 0.088 / Net I/σ(I): 10.5
Reflection shellResolution: 2.52→2.56 Å / Redundancy: 3.6 % / Rmerge(I) obs: 1.056 / Mean I/σ(I) obs: 2 / Num. unique obs: 103 / CC1/2: 0.53 / Rpim(I) all: 0.646 / Rrim(I) all: 1.243 / % possible all: 4.3

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Processing

Software
NameVersionClassification
BUSTER2.11.7refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
autoBUSTERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2I6L

2i6l
PDB Unreleased entry


Resolution: 2.52→48.08 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.903 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.336
RfactorNum. reflection% reflectionSelection details
Rfree0.251 1857 5.03 %RANDOM
Rwork0.198 ---
obs0.201 36931 82.2 %-
Displacement parametersBiso max: 174.05 Å2 / Biso mean: 70 Å2 / Biso min: 24.28 Å2
Baniso -1Baniso -2Baniso -3
1-8.3713 Å20 Å20 Å2
2---3.545 Å20 Å2
3----4.8263 Å2
Refine analyzeLuzzati coordinate error obs: 0.34 Å
Refinement stepCycle: final / Resolution: 2.52→48.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9141 0 116 189 9446
Biso mean--60.86 57.19 -
Num. residues----1154
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d3324SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1582HARMONIC5
X-RAY DIFFRACTIONt_it9485HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1224SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact9972SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d9485HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg12854HARMONIC21.14
X-RAY DIFFRACTIONt_omega_torsion2.76
X-RAY DIFFRACTIONt_other_torsion20.43
LS refinement shellResolution: 2.52→2.63 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.3022 33 4.47 %
Rwork0.2416 706 -
all0.2445 739 -
obs--14.66 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.8407-0.4031-0.79493.9662-0.62533.8750.0443-0.01660.1317-0.1454-0.0783-0.33210.09470.19140.0341-0.12240.01250.0098-0.27130.0266-0.171922.9517-11.5956-57.4866
21.81240.5673-0.07075.2311-0.45414.24660.01870.0399-0.27950.53950.089-0.0907-0.08620.2731-0.1078-0.0703-0.037-0.0189-0.1825-0.0435-0.304-5.9871-46.443-14.401
32.44841.7043-0.25484.09291.21553.04330.116-0.09470.10290.03170.1310.1645-0.36980.1525-0.2471-0.118-0.04840.0786-0.24710.0267-0.176914.541412.7825-37.3351
42.6612-0.50630.26263.0367-0.52184.41090.1136-0.07140.15930.1447-0.0227-0.02560.2285-0.3041-0.0909-0.0891-0.09310.0309-0.26820.0205-0.3044.2445-8.6876-11.7815
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A18 - 319
2X-RAY DIFFRACTION2{ B|* }B16 - 321
3X-RAY DIFFRACTION3{ C|* }C13 - 319
4X-RAY DIFFRACTION4{ D|* }D14 - 321

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