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- PDB-2hw6: Crystal structure of Mnk1 catalytic domain -

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Basic information

Entry
Database: PDB / ID: 2hw6
TitleCrystal structure of Mnk1 catalytic domain
ComponentsMAP kinase-interacting serine/threonine-protein kinase 1
KeywordsTRANSFERASE / protein kinase / drug design / mnk1 / phosphorylation
Function / homology
Function and homology information


calcium-dependent protein serine/threonine kinase activity / calmodulin-dependent protein kinase activity / Spry regulation of FGF signaling / regulation of translation / peptidyl-serine phosphorylation / calmodulin binding / non-specific serine/threonine protein kinase / intracellular signal transduction / protein phosphorylation / protein serine kinase activity ...calcium-dependent protein serine/threonine kinase activity / calmodulin-dependent protein kinase activity / Spry regulation of FGF signaling / regulation of translation / peptidyl-serine phosphorylation / calmodulin binding / non-specific serine/threonine protein kinase / 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
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
MAP kinase-interacting serine/threonine-protein kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsJauch, R. / Wahl, M.C.
CitationJournal: Embo J. / Year: 2006
Title: Mitogen-activated protein kinases interacting kinases are autoinhibited by a reprogrammed activation segment.
Authors: Jauch, R. / Cho, M.K. / Netter, C. / Schreiter, K. / Aicher, B. / Zweckstetter, M. / Wahl, M.C.
History
DepositionAug 1, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 29, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE RESIDUES 165-205 IN UNP Q9BUB5 ARE VARIAN AND ARE MISSING IN ISOFORM 2 AND ISOFORM 3.

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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-protein kinase 1
B: MAP kinase-interacting serine/threonine-protein kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,1484
Polymers68,9562
Non-polymers1922
Water2,486138
1
A: MAP kinase-interacting serine/threonine-protein kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5742
Polymers34,4781
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: MAP kinase-interacting serine/threonine-protein kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5742
Polymers34,4781
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)93.468, 93.468, 175.181
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Detailsthe asymmetric unit contains 2 molecules the biological unit is a monomer

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Components

#1: Protein MAP kinase-interacting serine/threonine-protein kinase 1 / MAP kinase signal-integrating kinase 1 / Mnk1


Mass: 34478.141 Da / Num. of mol.: 2 / Fragment: Mnk1-KR
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MKNK1, MNK1 / Plasmid: pGEX-4T1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9BUB5, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 138 / Source method: isolated from a natural source / Formula: H2O

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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: 2.77 Å3/Da / Density % sol: 55.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 5.6
Details: 20% PEG3350, 0.2M Ammonium sulfate, pH 5.6, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.98008 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Apr 4, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98008 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. all: 19844 / Num. obs: 18256 / % possible obs: 92.1 % / Observed criterion σ(F): 2

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2AC3

2ac3


Resolution: 2.5→30 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.908 / SU B: 20.494 / SU ML: 0.219 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.77 / ESU R Free: 0.344 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25701 937 4.9 %RANDOM
Rwork0.20666 ---
obs0.20911 18206 69.61 %-
all-19844 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.14 Å2
Baniso -1Baniso -2Baniso -3
1-1.46 Å20 Å20 Å2
2--1.46 Å20 Å2
3----2.93 Å2
Refinement stepCycle: LAST / Resolution: 2.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3815 0 10 138 3963
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223903
X-RAY DIFFRACTIONr_angle_refined_deg1.1741.9625262
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5595469
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.15924.309188
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.79215701
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5261522
X-RAY DIFFRACTIONr_chiral_restr0.0810.2571
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022929
X-RAY DIFFRACTIONr_nbd_refined0.2090.21847
X-RAY DIFFRACTIONr_nbtor_refined0.3070.22649
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1310.2145
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1520.223
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1650.26
X-RAY DIFFRACTIONr_mcbond_it0.5441.52414
X-RAY DIFFRACTIONr_mcangle_it0.99923787
X-RAY DIFFRACTIONr_scbond_it0.96431672
X-RAY DIFFRACTIONr_scangle_it1.6694.51475
LS refinement shellResolution: 2.5→2.57 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.469 10 -
Rwork0.333 161 -
obs--8.72 %
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)
11.7003-0.0818-1.27181.1868-1.01533.25410.0028-0.0257-0.13630.0287-0.1043-0.06930.1897-0.02930.10150.0155-0.0066-0.0036-0.05220.0147-0.074110.044843.313877.9509
22.20861.4335-0.80812.274-1.03072.5137-0.070.07970.00040.2016-0.0659-0.061-0.22850.12940.13580.0007-0.0027-0.0502-0.06530.0313-0.098822.988459.560963.2522
31.4476-0.88510.11252.33920.63324.39250.1021-0.0007-0.0003-0.023-0.08760.1564-0.1103-0.5448-0.0145-0.02550.06260.0230.0680.0312-0.1338-8.219453.024588.7415
41.74160.0016-0.74163.79471.26114.25420.04910.18530.22480.0868-0.0196-0.1527-0.9273-0.2387-0.02950.32390.14790.0469-0.16150.0451-0.1572-2.584871.5799102.9145
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA39 - 1275 - 93
2X-RAY DIFFRACTION2AA128 - 19694 - 162
3X-RAY DIFFRACTION2AA223 - 260189 - 226
4X-RAY DIFFRACTION2AA290 - 335256 - 301
5X-RAY DIFFRACTION3BB40 - 1276 - 93
6X-RAY DIFFRACTION4BB128 - 19694 - 162
7X-RAY DIFFRACTION4BB221 - 260187 - 226
8X-RAY DIFFRACTION4BB299 - 334265 - 300

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