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- PDB-9m1z: Crystal Structure of MAP2K6 complexed with 5Z-7-oxozeaenol -

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Basic information

Entry
Database: PDB / ID: 9m1z
TitleCrystal Structure of MAP2K6 complexed with 5Z-7-oxozeaenol
ComponentsDual specificity mitogen-activated protein kinase kinase 6
KeywordsTRANSFERASE / Mitogen-activated protein kinase kinase 6
Function / homology
Function and homology information


nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway / mitogen-activated protein kinase kinase / negative regulation of cold-induced thermogenesis / stress-activated protein kinase signaling cascade / Myogenesis / p38MAPK cascade / PI5P Regulates TP53 Acetylation / MAP kinase kinase activity / Uptake and function of anthrax toxins / stress-activated MAPK cascade ...nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway / mitogen-activated protein kinase kinase / negative regulation of cold-induced thermogenesis / stress-activated protein kinase signaling cascade / Myogenesis / p38MAPK cascade / PI5P Regulates TP53 Acetylation / MAP kinase kinase activity / Uptake and function of anthrax toxins / stress-activated MAPK cascade / cardiac muscle contraction / signal transduction in response to DNA damage / regulation of signal transduction by p53 class mediator / activated TAK1 mediates p38 MAPK activation / NOD1/2 Signaling Pathway / PKR-mediated signaling / bone development / Interleukin-1 signaling / cellular senescence / osteoblast differentiation / MAPK cascade / protein tyrosine kinase activity / Oxidative Stress Induced Senescence / cytoskeleton / positive regulation of MAPK cascade / regulation of cell cycle / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / protein kinase binding / signal transduction / nucleoplasm / ATP binding / identical protein binding / cytoplasm / cytosol
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
Chem-1FM / Dual specificity mitogen-activated protein kinase kinase 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsYumura, S. / Kinoshita, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)JP23ama121023 Japan
CitationJournal: To Be Published
Title: The discrepancies in amino acid sequence of the phosphate-binding loop lead to distinctive binding modes of a covalent inhibitor for MAP2K1 and MAP2K6: Structural insights for producing selective inhibitors
Authors: Yumura, S. / Kinoshita, T.
History
DepositionFeb 26, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 4, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)154,9268
Polymers153,4774
Non-polymers1,4494
Water1,45981
1
D: Dual specificity mitogen-activated protein kinase kinase 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7322
Polymers38,3691
Non-polymers3621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Dual specificity mitogen-activated protein kinase kinase 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7322
Polymers38,3691
Non-polymers3621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: Dual specificity mitogen-activated protein kinase kinase 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7322
Polymers38,3691
Non-polymers3621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
C: Dual specificity mitogen-activated protein kinase kinase 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7322
Polymers38,3691
Non-polymers3621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.347, 120.155, 106.317
Angle α, β, γ (deg.)90.00, 101.01, 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: 38369.195 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAP2K6, MEK6, MKK6, PRKMK6, SKK3 / Production host: Escherichia coli (E. coli)
References: UniProt: P52564, mitogen-activated protein kinase kinase
#2: Chemical
ChemComp-1FM / (3S,5Z,8S,9S,11E)-8,9,16-trihydroxy-14-methoxy-3-methyl-3,4,9,10-tetrahydro-1H-2-benzoxacyclotetradecine-1,7(8H)-dione / (5Z)-7-Oxozeaenol


Mass: 362.374 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C19H22O7 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / 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: 2.79 Å3/Da / Density % sol: 55.95 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Citrate pH5.0, 20% PEG4000, 0.2 M L-proline

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 26, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.95→47.861 Å / Num. obs: 34340 / % possible obs: 95.7 % / Redundancy: 3 % / CC1/2: 0.992 / Net I/σ(I): 4.83
Reflection shellResolution: 2.95→3.12 Å / Num. unique obs: 5348 / CC1/2: 0.251

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→47.86 Å / SU ML: 0.71 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 43.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3316 1556 5 %
Rwork0.2742 --
obs0.2771 31106 91.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3→47.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9111 0 104 81 9296
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008
X-RAY DIFFRACTIONf_angle_d0.805
X-RAY DIFFRACTIONf_dihedral_angle_d8.2561246
X-RAY DIFFRACTIONf_chiral_restr0.0461418
X-RAY DIFFRACTIONf_plane_restr0.0111625
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.10.49911140.50722113X-RAY DIFFRACTION72
3.1-3.210.47371250.47222409X-RAY DIFFRACTION83
3.21-3.340.42681440.40982699X-RAY DIFFRACTION93
3.34-3.490.40311490.37162819X-RAY DIFFRACTION97
3.49-3.670.39781490.33982840X-RAY DIFFRACTION97
3.67-3.90.38911490.27792819X-RAY DIFFRACTION97
3.9-4.20.33881480.26412828X-RAY DIFFRACTION97
4.2-4.620.30761460.25482770X-RAY DIFFRACTION94
4.63-5.290.28681440.24382770X-RAY DIFFRACTION94
5.29-6.670.40461430.27732737X-RAY DIFFRACTION93
6.67-47.860.24521450.20682746X-RAY DIFFRACTION92

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