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- PDB-6yf8: DYRK1A with PST001 -

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Basic information

Entry
Database: PDB / ID: 6yf8
TitleDYRK1A with PST001
ComponentsDual specificity tyrosine-phosphorylation-regulated kinase 1A
KeywordsTRANSFERASE / DYRK1A / Kinase
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 / protein serine/threonine/tyrosine kinase activity / RNA polymerase II CTD heptapeptide repeat 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 / actin binding / protein autophosphorylation / 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 / cytoplasm / cytosol
Similarity search - Function
Dual specificity tyrosine-phosphorylation-regulated kinase 1A/1B, catalytic domain / : / 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
Similarity search - Domain/homology
Chem-OPW / Dual specificity tyrosine-phosphorylation-regulated kinase 1A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.198 Å
AuthorsRothweiler, U.
CitationJournal: To Be Published
Title: DYRK1A with PST001
Authors: Rothweiler, U.
History
DepositionMar 26, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 7, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)171,8138
Polymers170,6164
Non-polymers1,1974
Water00
1
A: Dual specificity tyrosine-phosphorylation-regulated kinase 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9532
Polymers42,6541
Non-polymers2991
Water0
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)42,9532
Polymers42,6541
Non-polymers2991
Water0
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)42,9532
Polymers42,6541
Non-polymers2991
Water0
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)42,9532
Polymers42,6541
Non-polymers2991
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.000, 88.040, 229.720
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 / hMNB


Mass: 42653.992 Da / Num. of mol.: 4
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: Chemical
ChemComp-OPW / ~{N}-[5-(5-methoxy-1,3-benzothiazol-2-yl)pyridin-3-yl]ethanamide


Mass: 299.348 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H13N3O2S / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
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: 2.61 Å3/Da / Density % sol: 52.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
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 / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 3.198→50 Å / Num. obs: 30124 / % possible obs: 99.3 % / Redundancy: 6.66 % / CC1/2: 0.99 / Rrim(I) all: 0.29 / Net I/σ(I): 7
Reflection shellResolution: 3.198→3.39 Å / Num. unique obs: 4745 / CC1/2: 0.58

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4nct

4nct


Resolution: 3.198→48.298 Å / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.74
RfactorNum. reflection% reflection
Rfree0.2828 1460 4.85 %
Rwork0.2487 --
obs0.2509 30122 99.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.198→48.298 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10930 0 84 0 11014
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00311282
X-RAY DIFFRACTIONf_angle_d0.75315253
X-RAY DIFFRACTIONf_dihedral_angle_d3.9256703
X-RAY DIFFRACTIONf_chiral_restr0.051624
X-RAY DIFFRACTIONf_plane_restr0.0041944
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1998-3.3140.37911630.32642752X-RAY DIFFRACTION93
3.314-3.44650.34711290.29582872X-RAY DIFFRACTION96
3.4465-3.6030.30711460.28412809X-RAY DIFFRACTION95
3.603-3.79250.33111520.26972842X-RAY DIFFRACTION95
3.7925-4.02950.28231430.25522865X-RAY DIFFRACTION95
4.0295-4.33950.25551120.22812794X-RAY DIFFRACTION94
4.3395-4.77430.24991760.2192839X-RAY DIFFRACTION94
4.7743-5.46060.25831260.23392926X-RAY DIFFRACTION96
5.4606-6.86270.36071400.26912904X-RAY DIFFRACTION95
6.8627-27.84050.23051690.21443018X-RAY DIFFRACTION94
Refinement TLS params.Method: refined / Origin x: 14.4139 Å / Origin y: 7.3483 Å / Origin z: 28.9554 Å
111213212223313233
T0.7464 Å2-0.0797 Å2-0.0309 Å2-0.5328 Å20.0255 Å2--0.2693 Å2
L0.3726 °2-0.0421 °2-0.1745 °2-0.826 °20.0338 °2--1.0312 °2
S-0.0657 Å °0.0268 Å °-0.0248 Å °-0.3638 Å °0.0881 Å °0.087 Å °0.1178 Å °0.029 Å °-0.022 Å °
Refinement TLS groupSelection details: all

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