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- PDB-5a4e: DYRK1A in complex with methoxy benzothiazole fragment -

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Basic information

Entry
Database: PDB / ID: 5a4e
TitleDYRK1A in complex with methoxy benzothiazole fragment
ComponentsDUAL SPECIFICITY TYROSINE-PHOSPHORYLATION-REGULATED KINASE 1ADYRK1A
KeywordsTRANSFERASE
Function / homology
Function and homology information


histone H3T45 kinase activity / positive regulation of protein deacetylation / peptidyl-serine autophosphorylation / negative regulation of DNA methylation-dependent heterochromatin formation / dual-specificity kinase / [RNA-polymerase]-subunit kinase / negative regulation of microtubule polymerization / tau-protein kinase activity / negative regulation of mRNA splicing, via spliceosome / negative regulation of DNA damage response, signal transduction by p53 class mediator ...histone H3T45 kinase activity / positive regulation of protein deacetylation / peptidyl-serine autophosphorylation / negative regulation of DNA methylation-dependent heterochromatin formation / dual-specificity kinase / [RNA-polymerase]-subunit kinase / negative regulation of microtubule polymerization / tau-protein kinase activity / negative regulation of mRNA splicing, via spliceosome / negative regulation of DNA damage response, signal transduction by p53 class mediator / amyloid-beta formation / G0 and Early G1 / peptidyl-tyrosine autophosphorylation / cytoskeletal protein binding / protein serine/threonine/tyrosine kinase activity / tubulin binding / RNA polymerase II CTD heptapeptide repeat kinase activity / positive regulation of RNA splicing / peptidyl-threonine phosphorylation / tau protein binding / non-membrane spanning protein tyrosine kinase activity / circadian rhythm / peptidyl-tyrosine phosphorylation / : / nervous system development / actin binding / peptidyl-serine phosphorylation / protein tyrosine kinase activity / protein autophosphorylation / transcription coactivator activity / cytoskeleton / protein kinase activity / nuclear speck / ribonucleoprotein complex / axon / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / dendrite / positive regulation of DNA-templated transcription / nucleoplasm / ATP binding / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Dual specificity tyrosine-phosphorylation-regulated kinase 1A/1B, catalytic domain / 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 ...Dual specificity tyrosine-phosphorylation-regulated kinase 1A/1B, catalytic domain / 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
N-(5-methoxy-1,3-benzothiazol-2-yl)ethanamide / Dual specificity tyrosine-phosphorylation-regulated kinase 1A
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.68 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 8, 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 1.6Jan 10, 2024Group: 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_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)171,5058
Polymers170,6164
Non-polymers8894
Water1,62190
1
A: DUAL SPECIFICITY TYROSINE-PHOSPHORYLATION-REGULATED KINASE 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,8762
Polymers42,6541
Non-polymers2221
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)42,8762
Polymers42,6541
Non-polymers2221
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)42,8762
Polymers42,6541
Non-polymers2221
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)42,8762
Polymers42,6541
Non-polymers2221
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)87.083, 87.103, 226.956
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 / DYRK1A / 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-7QQ / N-(5-methoxy-1,3-benzothiazol-2-yl)ethanamide


Mass: 222.264 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H10N2O2S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 90 / 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: 2.5 Å3/Da / Density % sol: 51 %
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: 14.1 / Wavelength: 0.918409
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 24, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918409 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.702
11K, H, -L20.298
ReflectionResolution: 2.68→50 Å / Num. obs: 48593 / % possible obs: 98.5 % / Observed criterion σ(I): 1.55 / Redundancy: 5.3 % / Rmerge(I) obs: 0.16 / Net I/σ(I): 6.8
Reflection shellResolution: 2.68→2.84 Å / Redundancy: 5 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 1.55 / % possible all: 92.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4NCT

4nct


Resolution: 2.68→47.54 Å / Cor.coef. Fo:Fc: 0.894 / Cor.coef. Fo:Fc free: 0.846 / SU B: 18.503 / SU ML: 0.191 / Cross valid method: THROUGHOUT / ESU R: 0.208 / ESU R Free: 0.074 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.26784 2082 4.3 %RANDOM
Rwork0.23577 ---
obs0.2371 46552 98.54 %-
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: 57.057 Å2
Baniso -1Baniso -2Baniso -3
1--19.23 Å20 Å20 Å2
2--52.08 Å20 Å2
3----32.85 Å2
Refinement stepCycle: LAST / Resolution: 2.68→47.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10289 0 60 90 10439
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01910655
X-RAY DIFFRACTIONr_bond_other_d0.0010.0210224
X-RAY DIFFRACTIONr_angle_refined_deg0.9111.98414387
X-RAY DIFFRACTIONr_angle_other_deg0.6993.00323461
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.53951248
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.24723.952501
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.149151899
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4981563
X-RAY DIFFRACTIONr_chiral_restr0.0480.21526
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02111863
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022528
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_it0.6653.6615028
X-RAY DIFFRACTIONr_mcbond_other0.6653.665027
X-RAY DIFFRACTIONr_mcangle_it1.2165.4836264
X-RAY DIFFRACTIONr_mcangle_other1.2165.4836265
X-RAY DIFFRACTIONr_scbond_it0.3693.6785627
X-RAY DIFFRACTIONr_scbond_other0.3693.6785628
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.7055.5138124
X-RAY DIFFRACTIONr_long_range_B_refined2.42629.16612407
X-RAY DIFFRACTIONr_long_range_B_other2.4329.16612407
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.68→2.75 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.39 135 -
Rwork0.401 2831 -
obs--82.78 %
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)
10.2133-0.32990.21430.6104-0.19190.4677-0.0386-0.00750.03350.01590.0273-0.0627-0.013-0.02850.01130.2933-0.0130.00520.05750.01610.316-5.161720.8875-48.8625
20.24270.00820.45010.40820.03470.98770.13170.00840.0060.15670.0135-0.03790.14630.0028-0.14520.44650.0265-0.0550.0074-0.00320.2765-1.648619.6408-8.4404
30.3901-0.10940.09690.65760.15520.9426-0.07950.1093-0.10450.21410.00260.0348-0.00840.07360.07690.38060.02780.03140.0422-0.04670.2701-13.6906-17.0631-23.7021
40.08230.09510.00270.3348-0.30171.2671-0.04560.06570.03510.08960.11080.04390.0498-0.072-0.06510.3012-0.01440.04230.0675-0.00780.2906-39.2775.1746-37.2677
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A134 - 2044
2X-RAY DIFFRACTION2B133 - 2015
3X-RAY DIFFRACTION3C134 - 2009
4X-RAY DIFFRACTION4D134 - 2022

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