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- PDB-4nct: Human DYRK1A in complex with PKC412 -

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Basic information

Entry
Database: PDB / ID: 4nct
TitleHuman DYRK1A in complex with PKC412
Components(Dual specificity tyrosine-phosphorylation-regulated kinase 1A) x 2
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / Protein kinase / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


regulation of amyloid-beta formation / negative regulation of heterochromatin formation / regulation of neurofibrillary tangle assembly / histone H3T45 kinase activity / dual-specificity kinase / splicing factor binding / [RNA-polymerase]-subunit kinase / tau-protein kinase activity / regulation of alternative mRNA splicing, via spliceosome / negative regulation of microtubule polymerization ...regulation of amyloid-beta formation / negative regulation of heterochromatin formation / regulation of neurofibrillary tangle assembly / histone H3T45 kinase activity / dual-specificity kinase / splicing factor binding / [RNA-polymerase]-subunit kinase / tau-protein kinase activity / regulation of alternative mRNA splicing, via spliceosome / negative regulation of microtubule polymerization / negative regulation of DNA damage response, signal transduction by p53 class mediator / negative regulation of mRNA splicing, via spliceosome / G0 and Early G1 / cytoskeletal protein binding / RNA polymerase II CTD heptapeptide repeat kinase activity / protein serine/threonine/tyrosine kinase activity / tubulin binding / peptidyl-tyrosine phosphorylation / positive regulation of RNA splicing / non-membrane spanning protein tyrosine kinase activity / circadian rhythm / tau protein binding / nervous system development / protein autophosphorylation / actin binding / protein tyrosine kinase activity / transcription coactivator activity / protein phosphorylation / protein kinase activity / nuclear speck / ribonucleoprotein complex / axon / protein serine kinase activity / protein serine/threonine kinase activity / dendrite / centrosome / positive regulation of DNA-templated transcription / nucleoplasm / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Dual specificity tyrosine-phosphorylation-regulated kinase 1A/1B, catalytic domain / : / 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 ...Dual specificity tyrosine-phosphorylation-regulated kinase 1A/1B, catalytic domain / : / 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
PKC412 / Dual specificity tyrosine-phosphorylation-regulated kinase 1A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.597 Å
AuthorsAlexeeva, M.O. / Rothweiler, U.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2015
Title: The structure of a dual-specificity tyrosine phosphorylation-regulated kinase 1A-PKC412 complex reveals disulfide-bridge formation with the anomalous catalytic loop HRD(HCD) cysteine.
Authors: Alexeeva, M. / Aberg, E. / Engh, R.A. / Rothweiler, U.
History
DepositionOct 25, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2015Provider: repository / Type: Initial release
Revision 1.1May 20, 2015Group: Database references
Revision 1.2Jul 22, 2015Group: Database references
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _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: Dual specificity tyrosine-phosphorylation-regulated kinase 1A
B: Dual specificity tyrosine-phosphorylation-regulated kinase 1A
C: Dual specificity tyrosine-phosphorylation-regulated kinase 1A
D: Dual specificity tyrosine-phosphorylation-regulated kinase 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,9788
Polymers170,6964
Non-polymers2,2834
Water3,801211
1
A: Dual specificity tyrosine-phosphorylation-regulated kinase 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2252
Polymers42,6541
Non-polymers5711
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Dual specificity tyrosine-phosphorylation-regulated kinase 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2252
Polymers42,6541
Non-polymers5711
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Dual specificity tyrosine-phosphorylation-regulated kinase 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,3052
Polymers42,7341
Non-polymers5711
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Dual specificity tyrosine-phosphorylation-regulated kinase 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2252
Polymers42,6541
Non-polymers5711
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8540 Å2
ΔGint-19 kcal/mol
Surface area56510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.764, 87.895, 229.921
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Dual specificity tyrosine-phosphorylation-regulated kinase 1A / Dual specificity YAK1-related kinase / HP86 / Protein kinase minibrain homolog / MNBH / hMNB


Mass: 42653.992 Da / Num. of mol.: 3 / Fragment: Kinase domain DYRK1A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DYRK1A, DYRK, MNB, MNBH / Production host: Escherichia coli (E. coli) / References: UniProt: Q13627, dual-specificity kinase
#2: Protein Dual specificity tyrosine-phosphorylation-regulated kinase 1A / Dual specificity YAK1-related kinase / HP86 / Protein kinase minibrain homolog / MNBH / hMNB


Mass: 42733.969 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DYRK1A, DYRK, MNB, MNBH / Production host: Escherichia coli (E. coli) / References: UniProt: Q13627, dual-specificity kinase
#3: Chemical
ChemComp-2K2 / PKC412 / N-[(5S,6R,7R,9R)-6-methoxy-5-methyl-14-oxo-6,7,8,9,15,16-hexahydro-5H,14H-5,9-epoxy-4b,9a,15-triazadibenzo[b,h]cyclonon a[1,2,3,4-jkl]cyclopenta[e]-as-indacen-7-yl]-N-methylbenzamide


Mass: 570.637 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C35H30N4O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 211 / Source method: isolated from a natural source / Formula: H2O
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: 2.6 Å3/Da / Density % sol: 52.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 0.1 M KSCN; 0.05M LiCl; 10% PEG 3350, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918409 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 19, 2013
RadiationMonochromator: Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918409 Å / Relative weight: 1
ReflectionResolution: 2.597→48.25 Å / Num. all: 55797 / Num. obs: 55625 / % possible obs: 99.7 % / Observed criterion σ(I): -3
Reflection shell
Resolution (Å)Diffraction-ID% possible all
2.597-2.75198.7
2.75-2.941100
2.94-3.181100
3.18-3.48199.9
3.48-3.89199.9
3.89-4.48199.8

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Processing

Software
NameVersionClassification
MxCuBEdata collection
MOLREPphasing
REFMAC5.7.0032refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.597→48.25 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.906 / SU B: 15.625 / SU ML: 0.161 / Cross valid method: THROUGHOUT / ESU R: 0.147 / ESU R Free: 0.065 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24946 2782 5 %RANDOM
Rwork0.20805 ---
obs0.2101 52841 99.74 %-
all-52979 --
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: 49.922 Å2
Baniso -1Baniso -2Baniso -3
1--3.86 Å2-0 Å2-0 Å2
2--17.24 Å20 Å2
3----13.39 Å2
Refinement stepCycle: LAST / Resolution: 2.597→48.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11042 0 172 211 11425
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01911510
X-RAY DIFFRACTIONr_bond_other_d0.0010.0211043
X-RAY DIFFRACTIONr_angle_refined_deg1.111.99615586
X-RAY DIFFRACTIONr_angle_other_deg0.7083.00425364
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.35251339
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.72923.878539
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.694152050
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4491570
X-RAY DIFFRACTIONr_chiral_restr0.0620.21643
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02112783
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022735
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_it1.2223.3325386
X-RAY DIFFRACTIONr_mcbond_other1.2223.3325385
X-RAY DIFFRACTIONr_mcangle_it2.1454.996715
X-RAY DIFFRACTIONr_mcangle_other2.1414.9786716
X-RAY DIFFRACTIONr_scbond_it1.1243.516124
X-RAY DIFFRACTIONr_scbond_other1.1383.5076125
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.0315.2148872
X-RAY DIFFRACTIONr_long_range_B_refined3.99428.12213627
X-RAY DIFFRACTIONr_long_range_B_other3.97728.10613603
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.597→2.664 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.383 199 -
Rwork0.297 3770 -
obs--97.69 %
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)
10.6818-0.44670.05170.5565-0.27080.70150.0294-0.02010.05760.0772-0.0135-0.0698-0.03120.0206-0.01590.1343-0.02020.00410.0042-0.00020.18943.794416.6145-8.1031
20.50570.1068-0.03210.4734-0.45821.49790.00920.25030.07570.00360.104-0.025-0.0656-0.1783-0.11330.06580.02350.05170.1660.08470.112540.944121.7897-48.6633
31.16510.01710.05120.6642-0.27231.64440.11990.35570.10440.0089-0.10550.1501-0.1099-0.1413-0.01440.0360.06950.02060.17960.00030.18054.54969.7949-38.3618
40.69480.15180.20210.46020.0052.28830.09020.0786-0.18180.1207-0.0548-0.04090.24590.0407-0.03550.1535-0.00240.00290.0219-0.03140.20128.6175-17.2533-19.7946
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A134 - 480
2X-RAY DIFFRACTION1A501
3X-RAY DIFFRACTION1A601 - 668
4X-RAY DIFFRACTION2B133 - 480
5X-RAY DIFFRACTION2B501
6X-RAY DIFFRACTION2B601 - 638
7X-RAY DIFFRACTION3C134 - 479
8X-RAY DIFFRACTION3C501
9X-RAY DIFFRACTION3C601 - 642
10X-RAY DIFFRACTION4D134 - 480
11X-RAY DIFFRACTION4D501
12X-RAY DIFFRACTION4D601 - 663

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