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- PDB-5a3x: DYRK1A in complex with hydroxy benzothiazole fragment -

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Basic information

Entry
Database: PDB / ID: 5a3x
TitleDYRK1A in complex with hydroxy benzothiazole fragment
ComponentsDUAL SPECIFICITY TYROSINE-PHOSPHORYLATION-REGULATED KINASE 1A
KeywordsTRANSFERASE / PROTEIN KINASE
Function / homology
Function and homology information


negative regulation of heterochromatin formation / peptidyl-serine autophosphorylation / dual-specificity kinase / [RNA-polymerase]-subunit kinase / tau-protein kinase activity / negative regulation of microtubule polymerization / negative regulation of DNA damage response, signal transduction by p53 class mediator / amyloid-beta formation / negative regulation of mRNA splicing, via spliceosome / G0 and Early G1 ...negative regulation of heterochromatin formation / peptidyl-serine autophosphorylation / dual-specificity kinase / [RNA-polymerase]-subunit kinase / tau-protein kinase activity / negative regulation of microtubule polymerization / negative regulation of DNA damage response, signal transduction by p53 class mediator / amyloid-beta formation / negative regulation of mRNA splicing, via spliceosome / G0 and Early G1 / peptidyl-tyrosine autophosphorylation / cytoskeletal protein binding / RNA polymerase II CTD heptapeptide repeat kinase activity / peptidyl-threonine phosphorylation / protein serine/threonine/tyrosine kinase activity / tubulin binding / positive regulation of RNA splicing / non-membrane spanning protein tyrosine kinase activity / peptidyl-tyrosine phosphorylation / tau protein binding / circadian rhythm / nervous system development / peptidyl-serine phosphorylation / actin binding / protein autophosphorylation / protein tyrosine kinase activity / transcription coactivator activity / histone H3T45 kinase activity / protein kinase activity / nuclear speck / protein phosphorylation / axon / ribonucleoprotein complex / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / dendrite / 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
N-(5-oxidanyl-1,3-benzothiazol-2-yl)ethanamide / Dual specificity tyrosine-phosphorylation-regulated kinase 1A
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.26 Å
AuthorsRothweiler, U.
CitationJournal: J.Med.Chem. / Year: 2016
Title: Probing the ATP-Binding Pocket of Protein Kinase Dyrk1A with Benzothiazole Fragment Molecules
Authors: Rothweiler, U. / Stensen, W. / Brandsdal, B.O. / Isaksson, J. / Leeson, F.A. / Eugh, R.A. / Mjoen Svendsen, J.S.
History
DepositionJun 3, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 29, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 23, 2016Group: Database references
Revision 1.2Dec 14, 2016Group: Database references
Revision 1.3Dec 28, 2016Group: Database references
Revision 1.4Jan 30, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.5Feb 6, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.6Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / 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_leaving_atom_flag / _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)171,4498
Polymers170,6164
Non-polymers8334
Water4,089227
1
A: DUAL SPECIFICITY TYROSINE-PHOSPHORYLATION-REGULATED KINASE 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,8622
Polymers42,6541
Non-polymers2081
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: DUAL SPECIFICITY TYROSINE-PHOSPHORYLATION-REGULATED KINASE 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,8622
Polymers42,6541
Non-polymers2081
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: DUAL SPECIFICITY TYROSINE-PHOSPHORYLATION-REGULATED KINASE 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,8622
Polymers42,6541
Non-polymers2081
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: DUAL SPECIFICITY TYROSINE-PHOSPHORYLATION-REGULATED KINASE 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,8622
Polymers42,6541
Non-polymers2081
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)87.700, 88.420, 229.450
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.: 4 / Fragment: RESIDUES 126-490
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): RIL / References: UniProt: Q13627, dual-specificity kinase
#2: Chemical
ChemComp-QIV / N-(5-oxidanyl-1,3-benzothiazol-2-yl)ethanamide


Mass: 208.237 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H8N2O2S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 227 / 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: 53 % / Description: NONE
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 0.1 M KSCN; 0.1M KCL; 14% 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: 14.2 / Wavelength: 0.9184
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 26, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.711
11K, H, -L20.289
ReflectionResolution: 2.28→50 Å / Num. obs: 82115 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 7 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 10

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 2.26→48.29 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.902 / SU B: 12.007 / SU ML: 0.158 / Cross valid method: THROUGHOUT / ESU R: 0.068 / ESU R Free: 0.048 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.25867 4157 5.1 %RANDOM
Rwork0.23484 ---
obs0.23604 77936 97.73 %-
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: 47.633 Å2
Baniso -1Baniso -2Baniso -3
1-8.9 Å20 Å20 Å2
2--21.22 Å20 Å2
3----30.13 Å2
Refinement stepCycle: LAST / Resolution: 2.26→48.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11040 0 56 227 11323
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.01911362
X-RAY DIFFRACTIONr_bond_other_d0.0010.0210943
X-RAY DIFFRACTIONr_angle_refined_deg0.931.97715337
X-RAY DIFFRACTIONr_angle_other_deg0.6773.00125152
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.02751340
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.82923.903538
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.47152054
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0061569
X-RAY DIFFRACTIONr_chiral_restr0.0510.21629
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02112654
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022693
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_it0.5943.3385390
X-RAY DIFFRACTIONr_mcbond_other0.5943.3385389
X-RAY DIFFRACTIONr_mcangle_it1.05456720
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.4213.3715972
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: 2.263→2.322 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 207 -
Rwork0.286 3972 -
obs--68.27 %
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)
10.58360.3810.05110.30740.17990.4192-0.0066-0.02460.0371-0.0219-0.0110.0495-0.0110.00390.01760.05570.0196-0.00750.0277-0.00330.24060.639416.64658.0251
20.22790.09420.1740.25680.51771.1601-0.0163-0.19240.0199-0.01360.0770.02010.00520.1984-0.06070.03030.00750.00840.2856-0.0550.16562.976121.425148.6619
30.3665-0.19890.2610.2786-0.190.80540.0775-0.1336-0.0048-0.0057-0.0935-0.0584-0.12990.00660.01590.0837-0.08970.02080.22170.01610.210139.830110.11537.5838
40.2535-0.03490.17080.1061-0.01371.63760.1191-0.0604-0.0901-0.0626-0.07930.01620.19170.0255-0.03970.09140.0151-0.02140.08840.02540.240115.8162-17.311219.8526
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A134 - 481
2X-RAY DIFFRACTION2B133 - 481
3X-RAY DIFFRACTION3C134 - 481
4X-RAY DIFFRACTION4D134 - 480

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