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- PDB-1s9i: X-ray structure of the human mitogen-activated protein kinase kin... -

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Basic information

Entry
Database: PDB / ID: 1s9i
TitleX-ray structure of the human mitogen-activated protein kinase kinase 2 (MEK2)in a complex with ligand and MgATP
ComponentsDual specificity mitogen-activated protein kinase kinase 2
KeywordsTRANSFERASE / PROTEIN KINASE-LIGAND-MgATP COMPLEX / PROTEIN-PROTEIN INTERACTIONS
Function / homology
Function and homology information


epithelial cell proliferation involved in lung morphogenesis / regulation of axon regeneration / mitogen-activated protein kinase kinase / peptidyl-serine autophosphorylation / MAP-kinase scaffold activity / Signaling by MAP2K mutants / positive regulation of cell motility / regulation of Golgi inheritance / peroxisomal membrane / trachea formation ...epithelial cell proliferation involved in lung morphogenesis / regulation of axon regeneration / mitogen-activated protein kinase kinase / peptidyl-serine autophosphorylation / MAP-kinase scaffold activity / Signaling by MAP2K mutants / positive regulation of cell motility / regulation of Golgi inheritance / peroxisomal membrane / trachea formation / Negative feedback regulation of MAPK pathway / regulation of early endosome to late endosome transport / positive regulation of axonogenesis / regulation of stress-activated MAPK cascade / Frs2-mediated activation / ERBB2-ERBB3 signaling pathway / face development / MAPK1 (ERK2) activation / MAP kinase kinase activity / thyroid gland development / Uptake and function of anthrax toxins / Schwann cell development / ERK1 and ERK2 cascade / protein serine/threonine/tyrosine kinase activity / myelination / protein serine/threonine kinase activator activity / insulin-like growth factor receptor signaling pathway / thymus development / Signal transduction by L1 / PDZ domain binding / RAF activation / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / positive regulation of protein serine/threonine kinase activity / cytoplasmic side of plasma membrane / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / MAPK cascade / Signaling by BRAF and RAF1 fusions / cell-cell junction / late endosome / heart development / scaffold protein binding / protein tyrosine kinase activity / microtubule / early endosome / protein serine kinase activity / focal adhesion / protein serine/threonine kinase activity / positive regulation of gene expression / positive regulation of DNA-templated transcription / perinuclear region of cytoplasm / Golgi apparatus / endoplasmic reticulum / mitochondrion / extracellular region / ATP binding / nucleus / metal ion binding / cytosol
Similarity search - Function
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. ...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-5EA / ADENOSINE-5'-TRIPHOSPHATE / Dual specificity mitogen-activated protein kinase kinase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsOhren, J.F. / Chen, H. / Pavlovsky, A. / Whitehead, C. / Yan, C. / McConnell, P. / Delaney, A. / Dudley, D.T. / Sebolt-Leopold, J. / Hasemann, C.A.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2004
Title: Structures of human MAP kinase kinase 1 (MEK1) and MEK2 describe novel noncompetitive kinase inhibition.
Authors: Ohren, J.F. / Chen, H. / Pavlovsky, A. / Whitehead, C. / Zhang, E. / Kuffa, P. / Yan, C. / McConnell, P. / Spessard, C. / Banotai, C. / Mueller, W.T. / Delaney, A. / Omer, C. / Sebolt- ...Authors: Ohren, J.F. / Chen, H. / Pavlovsky, A. / Whitehead, C. / Zhang, E. / Kuffa, P. / Yan, C. / McConnell, P. / Spessard, C. / Banotai, C. / Mueller, W.T. / Delaney, A. / Omer, C. / Sebolt-Leopold, J. / Dudley, D.T. / Leung, I.K. / Flamme, C. / Warmus, J. / Kaufman, M. / Barrett, S. / Tecle, H. / Hasemann, C.A.
History
DepositionFeb 4, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 23, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dual specificity mitogen-activated protein kinase kinase 2
B: Dual specificity mitogen-activated protein kinase kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,3468
Polymers79,1932
Non-polymers2,1546
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5500 Å2
ΔGint-31 kcal/mol
Surface area28410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)161.888, 161.888, 122.986
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
DetailsThe NH2-truncated MEK2 is a homodimer in solution and in the crystallographic asu. MEK2 may form a functional dimer in vivo.

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Components

#1: Protein Dual specificity mitogen-activated protein kinase kinase 2 / MAP kinase kinase 2 / MAPKK 2 / ERK activator kinase 2 / MAPK/ERK kinase 2 / MEK2


Mass: 39596.363 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAP2K2, PRKMK2, MEK2, MKK2 / Plasmid: pET24b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P36507, EC: 2.7.1.37
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Chemical ChemComp-5EA / 5-{3,4-DIFLUORO-2-[(2-FLUORO-4-IODOPHENYL)AMINO]PHENYL}-N-(2-MORPHOLIN-4-YLETHYL)-1,3,4-OXADIAZOL-2-AMINE


Mass: 545.297 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H19F3IN5O2

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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: 2.94 Å3/Da / Density % sol: 58.12 %
Crystal growTemperature: 288 K / pH: 7
Details: Sodium / Potassium phosphate, DTT, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 288K, pH 7.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 2, 2002
RadiationMonochromator: SAGITALLY FOCUSED SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→14.4 Å / Num. obs: 15147 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 9.8 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 25.6
Reflection shellResolution: 3.2→3.28 Å / Rmerge(I) obs: 0.368 / Mean I/σ(I) obs: 6 / % possible all: 1

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Processing

Software
NameVersionClassification
HKL-2000data collection
TRUNCATEdata reduction
MOLREPphasing
REFMAC5.1.24refinement
HKL-2000data reduction
CCP4(TRUNCATE)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: HUMAN MAP2K1

Resolution: 3.2→14.4 Å / Cor.coef. Fo:Fc: 0.85 / Cor.coef. Fo:Fc free: 0.772 / SU B: 30.11 / SU ML: 0.534 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R Free: 0.667 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: MAXIMUM LIKELIHOOD REFINEMENT USING REFMAC 5.1.24
RfactorNum. reflection% reflectionSelection details
Rfree0.36374 802 5 %RANDOM
Rwork0.29028 ---
obs0.29401 15147 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 41.694 Å2
Baniso -1Baniso -2Baniso -3
1--1.36 Å2-0.68 Å20 Å2
2---1.36 Å20 Å2
3---2.04 Å2
Refinement stepCycle: LAST / Resolution: 3.2→14.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4686 0 126 0 4812
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0214889
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2171.9996601
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4355588
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_chiral_restr0.0720.2718
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.023655
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1950.22388
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.130.2142
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1820.230
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0490.21
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.3551.52953
X-RAY DIFFRACTIONr_mcangle_it0.65924774
X-RAY DIFFRACTIONr_scbond_it0.64631936
X-RAY DIFFRACTIONr_scangle_it1.1754.51827
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.201→3.28 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.482 52
Rwork0.335 1055

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