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- PDB-4azf: Human DYRK2 in complex with Leucettine L41 -

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Basic information

Entry
Database: PDB / ID: 4azf
TitleHuman DYRK2 in complex with Leucettine L41
ComponentsDYRK2 DUAL-SPECIFICITY TYROSINE-PHOSPHORYLATION REGULATED KINASE 2
KeywordsTRANSFERASE
Function / homology
Function and homology information


dual-specificity kinase / negative regulation of calcineurin-NFAT signaling cascade / smoothened signaling pathway / positive regulation of glycogen biosynthetic process / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / ubiquitin ligase complex / protein serine/threonine/tyrosine kinase activity / regulation of signal transduction by p53 class mediator / manganese ion binding / protein tyrosine kinase activity ...dual-specificity kinase / negative regulation of calcineurin-NFAT signaling cascade / smoothened signaling pathway / positive regulation of glycogen biosynthetic process / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / ubiquitin ligase complex / protein serine/threonine/tyrosine kinase activity / regulation of signal transduction by p53 class mediator / manganese ion binding / protein tyrosine kinase activity / Regulation of TP53 Activity through Phosphorylation / cytoskeleton / ribonucleoprotein complex / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / DNA damage response / magnesium ion binding / nucleoplasm / ATP binding / nucleus / cytoplasm / cytosol
Similarity search - Function
DYRK / Dual specificity tyrosine-phosphorylation-regulated kinase / Trypsin Inhibitor V; Chain A / 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 ...DYRK / Dual specificity tyrosine-phosphorylation-regulated kinase / Trypsin Inhibitor V; Chain A / 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-3RA / PHOSPHATE ION / Dual specificity tyrosine-phosphorylation-regulated kinase 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsElkins, J.M. / Soundararajan, M. / Muniz, J.R.C. / Tahtouh, T. / Burgy, G. / Durieu, E. / Lozach, O. / Cochet, C. / Schmid, R.S. / Lo, D.C. ...Elkins, J.M. / Soundararajan, M. / Muniz, J.R.C. / Tahtouh, T. / Burgy, G. / Durieu, E. / Lozach, O. / Cochet, C. / Schmid, R.S. / Lo, D.C. / Delhommel, F. / Carreaux, F. / Bazureau, J.P. / Meijer, L. / Edwards, A. / Bountra, C. / Knapp, S.
CitationJournal: J.Med.Chem. / Year: 2012
Title: Selectivity, Co-Crystal Structures and Neuroprotective Properties of Leucettines, a Family of Protein Kinase Inhibitors Derived from the Marine Sponge Alkaloid Leucettamine B.
Authors: Tahtouh, T. / Elkins, J.M. / Filippakopoulos, P. / Soundararajan, M. / Burgy, G. / Durieu, E. / Cochet, C. / Schmid, R.S. / Lo, D.C. / Delhommel, F. / Oberholzer, A. / Laurence, P. / ...Authors: Tahtouh, T. / Elkins, J.M. / Filippakopoulos, P. / Soundararajan, M. / Burgy, G. / Durieu, E. / Cochet, C. / Schmid, R.S. / Lo, D.C. / Delhommel, F. / Oberholzer, A. / Laurence, P. / Carreaux, F. / Bazureau, J.P. / Knapp, S. / Meijer, L.
History
DepositionJun 25, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 5, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2012Group: Database references / Other
Revision 1.2Nov 21, 2012Group: Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_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_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DYRK2 DUAL-SPECIFICITY TYROSINE-PHOSPHORYLATION REGULATED KINASE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7524
Polymers48,2871
Non-polymers4643
Water1,02757
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)83.461, 83.461, 148.534
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11A-2007-

HOH

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Components

#1: Protein DYRK2 DUAL-SPECIFICITY TYROSINE-PHOSPHORYLATION REGULATED KINASE 2 / DYRK2


Mass: 48287.363 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q92630, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-3RA / 5-(1,3-benzodioxol-5-ylmethyl)-2-(phenylamino)-4H-imidazol-4-one


Mass: 307.303 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H13N3O3
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / 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: 2.7 Å3/Da / Density % sol: 54.4 % / Description: NONE
Crystal growpH: 7.5
Details: 0.2 M NA/KPO4, 20% PEG 3350, 10% ETHYLENE GLYCOL, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.979
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 7, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.55→59.02 Å / Num. obs: 17843 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 12
Reflection shellResolution: 2.55→2.69 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.88 / Mean I/σ(I) obs: 2.5 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
MOSFLMdata reduction
SCALAdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3K2L

3k2l


Resolution: 2.55→74.27 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.914 / SU B: 20.845 / SU ML: 0.224 / Cross valid method: THROUGHOUT / ESU R: 0.489 / ESU R Free: 0.293 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.25515 907 5.1 %RANDOM
Rwork0.19681 ---
obs0.19973 16896 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 54.655 Å2
Baniso -1Baniso -2Baniso -3
1-1.34 Å20 Å20 Å2
2--1.34 Å20 Å2
3----2.68 Å2
Refinement stepCycle: LAST / Resolution: 2.55→74.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3222 0 32 57 3311
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.023340
X-RAY DIFFRACTIONr_bond_other_d0.0010.022271
X-RAY DIFFRACTIONr_angle_refined_deg1.3781.9734521
X-RAY DIFFRACTIONr_angle_other_deg0.8593.0015499
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8715407
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.85823.677155
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.115555
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0541521
X-RAY DIFFRACTIONr_chiral_restr0.0690.2475
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213716
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02691
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
LS refinement shellResolution: 2.55→2.616 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 61 -
Rwork0.282 1081 -
obs--99.91 %
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)
12.6748-0.32580.93352.31540.07397.8647-0.1146-0.513-0.37790.2509-0.09390.05990.13130.02270.20850.13480.037-0.05840.30790.08120.138557.64726.50237.249
28.22440.3175-0.62720.6934-0.0211.9089-0.08070.2894-0.1969-0.2992-0.02590.1538-0.04570.03970.10660.1790.0201-0.09740.0158-0.01740.062245.20227.59321.283
32.4238-0.24570.86831.5497-0.29063.6536-0.1379-0.1020.23620.0531-0.08960.1982-0.1315-0.4850.22750.02380.04-0.0080.1262-0.04110.066112.97728.70111.921
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A51 - 91
2X-RAY DIFFRACTION2A92 - 231
3X-RAY DIFFRACTION3A232 - 467

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