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- PDB-8pm3: Crystal structure of MAP2K6 with a covalent compound GCL94 -

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Basic information

Entry
Database: PDB / ID: 8pm3
TitleCrystal structure of MAP2K6 with a covalent compound GCL94
ComponentsDual specificity mitogen-activated protein kinase kinase 6
KeywordsTRANSFERASE / Kinase / Covalent / inhibitor / MAP2K6 / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway / mitogen-activated protein kinase kinase / stress-activated protein kinase signaling cascade / negative regulation of cold-induced thermogenesis / Myogenesis / PI5P Regulates TP53 Acetylation / p38MAPK cascade / MAP kinase kinase activity / Uptake and function of anthrax toxins / signal transduction in response to DNA damage ...nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway / mitogen-activated protein kinase kinase / stress-activated protein kinase signaling cascade / negative regulation of cold-induced thermogenesis / Myogenesis / PI5P Regulates TP53 Acetylation / p38MAPK cascade / MAP kinase kinase activity / Uptake and function of anthrax toxins / signal transduction in response to DNA damage / stress-activated MAPK cascade / cardiac muscle contraction / activated TAK1 mediates p38 MAPK activation / regulation of signal transduction by p53 class mediator / NOD1/2 Signaling Pathway / bone development / PKR-mediated signaling / Interleukin-1 signaling / osteoblast differentiation / cellular senescence / MAPK cascade / Oxidative Stress Induced Senescence / protein tyrosine kinase activity / cytoskeleton / regulation of cell cycle / positive regulation of MAPK cascade / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / protein kinase binding / signal transduction / nucleoplasm / ATP binding / identical protein binding / cytosol / cytoplasm
Similarity search - Function
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
~{N}-[3-(2-azanylpyridin-4-yl)phenyl]propanamide / Dual specificity mitogen-activated protein kinase kinase 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsWang, G.Q. / Seidler, N. / Roehm, S. / Gehringer, M. / Knapp, S. / Structural Genomics Consortium (SGC)
Funding support Canada, 1items
OrganizationGrant numberCountry
The Structural Genomics Consortium (SGC) Canada
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2025
Title: Probing the Protein Kinases' Cysteinome by Covalent Fragments.
Authors: Wang, G. / Seidler, N.J. / Rohm, S. / Pan, Y. / Liang, X.J. / Haarer, L. / Berger, B.T. / Sivashanmugam, S.A. / Wydra, V.R. / Forster, M. / Laufer, S.A. / Chaikuad, A. / Gehringer, M. / Knapp, S.
History
DepositionJun 28, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 20, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 1.2Jan 8, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Feb 26, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.year / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dual specificity mitogen-activated protein kinase kinase 6
B: Dual specificity mitogen-activated protein kinase kinase 6
C: Dual specificity mitogen-activated protein kinase kinase 6
D: Dual specificity mitogen-activated protein kinase kinase 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,9658
Polymers131,0004
Non-polymers9654
Water7,602422
1
A: Dual specificity mitogen-activated protein kinase kinase 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,9912
Polymers32,7501
Non-polymers2411
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Dual specificity mitogen-activated protein kinase kinase 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,9912
Polymers32,7501
Non-polymers2411
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Dual specificity mitogen-activated protein kinase kinase 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,9912
Polymers32,7501
Non-polymers2411
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Dual specificity mitogen-activated protein kinase kinase 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,9912
Polymers32,7501
Non-polymers2411
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.328, 97.529, 104.550
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Dual specificity mitogen-activated protein kinase kinase 6 / MAP kinase kinase 6 / MAPKK 6 / MAPK/ERK kinase 6 / MEK 6 / Stress-activated protein kinase kinase ...MAP kinase kinase 6 / MAPKK 6 / MAPK/ERK kinase 6 / MEK 6 / Stress-activated protein kinase kinase 3 / SAPK kinase 3 / SAPKK-3 / SAPKK3


Mass: 32749.885 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: LIG is a covalent compound / Source: (gene. exp.) Homo sapiens (human) / Gene: MAP2K6, MEK6, MKK6, PRKMK6, SKK3 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P52564, mitogen-activated protein kinase kinase
#2: Chemical
ChemComp-ZLE / ~{N}-[3-(2-azanylpyridin-4-yl)phenyl]propanamide


Mass: 241.288 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H15N3O / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 422 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.57 Å3/Da / Density % sol: 52.09 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.05M magnesium chloride -- 30% PEG500MME -- 0.1M HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.00003 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 1, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 2→48.62 Å / Num. obs: 88885 / % possible obs: 98.9 % / Redundancy: 5.8 % / CC1/2: 0.99 / Net I/σ(I): 13.4
Reflection shellResolution: 2→2.04 Å / Mean I/σ(I) obs: 2.6 / Num. unique obs: 4551 / CC1/2: 0.88 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0411refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→48.62 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.933 / SU B: 3.921 / SU ML: 0.108 / Cross valid method: THROUGHOUT / ESU R: 0.174 / ESU R Free: 0.158 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23615 4522 5.1 %RANDOM
Rwork0.1957 ---
obs0.19771 84350 98.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.296 Å2
Baniso -1Baniso -2Baniso -3
1--0.93 Å2-0 Å21.07 Å2
2--0.53 Å20 Å2
3---0.39 Å2
Refinement stepCycle: 1 / Resolution: 2→48.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8665 0 0 422 9087
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0128851
X-RAY DIFFRACTIONr_bond_other_d0.0010.0168578
X-RAY DIFFRACTIONr_angle_refined_deg1.5091.64711961
X-RAY DIFFRACTIONr_angle_other_deg0.5171.57219822
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.52751078
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.4576.15452
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.48101595
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0770.21347
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0210002
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021902
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.1433.2594348
X-RAY DIFFRACTIONr_mcbond_other3.1433.2584347
X-RAY DIFFRACTIONr_mcangle_it4.4385.8215414
X-RAY DIFFRACTIONr_mcangle_other4.4395.8215415
X-RAY DIFFRACTIONr_scbond_it4.0943.6774503
X-RAY DIFFRACTIONr_scbond_other4.0943.6774504
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.1096.576548
X-RAY DIFFRACTIONr_long_range_B_refined7.47632.2910231
X-RAY DIFFRACTIONr_long_range_B_other7.45932.0110188
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 334 -
Rwork0.238 6223 -
obs--99.24 %

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