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- PDB-5wvd: Structure of Mnk1 in complex with DS12881479 -

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Basic information

Entry
Database: PDB / ID: 5wvd
TitleStructure of Mnk1 in complex with DS12881479
ComponentsMAP kinase interacting serine/threonine kinase 1
KeywordsTRANSFERASE / kinase / kinase inhibitor / inactive conformation
Function / homology
Function and homology information


calcium-dependent protein serine/threonine kinase activity / calcium/calmodulin-dependent protein kinase activity / Spry regulation of FGF signaling / regulation of translation / peptidyl-serine phosphorylation / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity ...calcium-dependent protein serine/threonine kinase activity / calcium/calmodulin-dependent protein kinase activity / Spry regulation of FGF signaling / regulation of translation / peptidyl-serine phosphorylation / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / calmodulin binding / intracellular signal transduction / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / nucleoplasm / ATP binding / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
: / 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 ...: / 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-7UX / MAP kinase-interacting serine/threonine-protein kinase 1 / MAP kinase-interacting serine/threonine-protein kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsMatsui, Y. / Hanzawa, H.
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2018
Title: A novel inhibitor stabilizes the inactive conformation of MAPK-interacting kinase 1.
Authors: Matsui, Y. / Yasumatsu, I. / Yoshida, K.I. / Iimura, S. / Ikeno, Y. / Nawano, T. / Fukano, H. / Ubukata, O. / Hanzawa, H. / Tanzawa, F. / Isoyama, T.
History
DepositionDec 24, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 3, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 14, 2018Group: 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Nov 22, 2023Group: 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MAP kinase interacting serine/threonine kinase 1
B: MAP kinase interacting serine/threonine kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,1905
Polymers69,4912
Non-polymers6993
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2880 Å2
ΔGint-11 kcal/mol
Surface area21290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.635, 92.635, 174.437
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSGLYGLY3AA43 - 5612 - 25
21LYSLYSGLYGLY3BB43 - 5612 - 25
12GLYGLYLEULEU3AA58 - 12727 - 96
22GLYGLYLEULEU3BB58 - 12727 - 96
13SERSERPROPRO3AA148 - 258117 - 227
23SERSERPROPRO3BB148 - 258117 - 227
14ASPASPTRPTRP5AA308 - 332277 - 301
24ASPASPTRPTRP5BB308 - 332277 - 301

NCS ensembles :
ID
1
2

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Components

#1: Protein MAP kinase interacting serine/threonine kinase 1


Mass: 34745.465 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 37-341
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MKNK1 / Production host: Escherichia coli (E. coli) / References: UniProt: B5BUJ6, UniProt: Q9BUB5*PLUS
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-7UX / 1-methyl-N-(5-phenyl-1,3-thiazol-2-yl)piperidine-4-carboxamide


Mass: 301.407 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H19N3OS

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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: 2.69 Å3/Da / Density % sol: 54.32 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: polyethylene glycol 3350, ammonium sulfate, citrate buffer (pH 6.2), MgCl2

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 22, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 15900 / % possible obs: 99.9 % / Redundancy: 7.1 % / Net I/σ(I): 18.6
Reflection shellResolution: 3→3.11 Å / Redundancy: 7.2 % / Mean I/σ(I) obs: 3.4 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2HW6

2hw6


Resolution: 3→20 Å / Cor.coef. Fo:Fc: 0.902 / Cor.coef. Fo:Fc free: 0.878 / SU B: 36.894 / SU ML: 0.315 / Cross valid method: THROUGHOUT / ESU R Free: 0.428
RfactorNum. reflection% reflectionSelection details
Rfree0.27121 1581 10 %RANDOM
Rwork0.2389 ---
obs0.24215 14265 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 62.197 Å2
Baniso -1Baniso -2Baniso -3
1-2.07 Å20 Å20 Å2
2--2.07 Å2-0 Å2
3----4.13 Å2
Refinement stepCycle: 1 / Resolution: 3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3628 0 47 0 3675
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0193750
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5341.9755051
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9965445
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.21924.294177
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.83315664
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4781521
X-RAY DIFFRACTIONr_chiral_restr0.1070.2547
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212842
X-RAY DIFFRACTIONr_gen_planes_other
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
100medium positional0.120.5
785loose positional0.165
680tight thermal2.460.5
100medium thermal2.352
785loose thermal2.2810
LS refinement shellResolution: 3→3.076 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 102 -
Rwork0.341 999 -
obs--99.37 %
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)
12.2606-1.69352.18092.8476-2.3225.2154-0.0756-0.17310.1961-0.0103-0.00830.0947-0.1635-0.22210.08380.0481-0.029-0.020.0842-0.03780.1991-7.2059-28.310525.0015
23.8830.5633-1.94481.1869-0.45966.5927-0.1112-0.3449-0.1048-0.06550.07650.43820.5846-1.06520.03470.1958-0.1869-0.05970.51850.10540.351-15.9203-50.544854.1284
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A41 - 334
2X-RAY DIFFRACTION2B41 - 333

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