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- PDB-5a4q: DYRK1A IN COMPLEX WITH CHLORO BENZOTHIAZOLE FRAGMENT -

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Basic information

Entry
Database: PDB / ID: 5a4q
TitleDYRK1A IN COMPLEX WITH CHLORO BENZOTHIAZOLE FRAGMENT
ComponentsDUAL SPECIFICITY TYROSINE-PHOSPHORYLATION-REGULATED KINASE 1A
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 / amyloid-beta formation / 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 / amyloid-beta formation / negative regulation of DNA damage response, signal transduction by p53 class mediator / negative regulation of mRNA splicing, via spliceosome / 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 / non-membrane spanning protein tyrosine kinase activity / tau protein binding / peptidyl-tyrosine phosphorylation / circadian rhythm / 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 / protein phosphorylation / axon / 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 ...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-CHLORANYL-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: 2.37 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 11, 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
Revision 1.7Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)171,5238
Polymers170,6164
Non-polymers9074
Water6,215345
1
A: DUAL SPECIFICITY TYROSINE-PHOSPHORYLATION-REGULATED KINASE 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,8812
Polymers42,6541
Non-polymers2271
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)42,8812
Polymers42,6541
Non-polymers2271
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)42,8812
Polymers42,6541
Non-polymers2271
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)42,8812
Polymers42,6541
Non-polymers2271
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)88.039, 88.938, 229.759
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: UNP 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-Y3L / N-(5-CHLORANYL-1,3-BENZOTHIAZOL-2-YL)ETHANAMIDE


Mass: 226.683 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H7ClN2OS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 345 / 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: 2.65 Å3/Da / Density % sol: 53.5 % / Description: NONE
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 0.1 M KSCN; 0.1M NACL; 16% 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
ReflectionResolution: 2.37→50 Å / Num. obs: 73459 / % possible obs: 99.3 % / Observed criterion σ(I): 2.26 / Redundancy: 6.4 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 13.62
Reflection shellResolution: 2.37→2.52 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.74 / Mean I/σ(I) obs: 2.26 / % possible all: 96.4

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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: 2.37→48.45 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.92 / SU B: 11.014 / SU ML: 0.137 / Cross valid method: THROUGHOUT / ESU R: 0.07 / ESU R Free: 0.049 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.24251 2101 2.9 %RANDOM
Rwork0.2066 ---
obs0.20764 71357 99.33 %-
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: 48.573 Å2
Baniso -1Baniso -2Baniso -3
1--8.92 Å20 Å20 Å2
2--23.01 Å20 Å2
3----14.1 Å2
Refinement stepCycle: LAST / Resolution: 2.37→48.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10917 0 56 345 11318
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01911236
X-RAY DIFFRACTIONr_bond_other_d0.0010.0210702
X-RAY DIFFRACTIONr_angle_refined_deg1.371.97415191
X-RAY DIFFRACTIONr_angle_other_deg0.773.00124563
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9851335
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.04823.977533
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.629151967
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7791565
X-RAY DIFFRACTIONr_chiral_restr0.0750.21623
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02112596
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022677
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_it1.9393.4335373
X-RAY DIFFRACTIONr_mcbond_other1.9393.4335372
X-RAY DIFFRACTIONr_mcangle_it3.1245.1386697
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.1433.6525863
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: 2.372→2.433 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 142 -
Rwork0.283 4800 -
obs--91.98 %
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)
10.86560.5178-0.25080.3266-0.2050.78210.0363-0.0443-0.0036-0.0101-0.0381-0.0143-0.03410.00010.00180.0960.0360.01020.02130.00530.0986-0.4088-16.7098.0372
20.7060.3684-0.38550.5306-0.85332.07880.0213-0.10220.0021-0.02810.15690.060.0347-0.2726-0.17820.0568-0.006-0.01110.19910.06320.0606-2.4641-20.792648.8442
31.23130.2028-0.11880.320.13171.85180.0477-0.4484-0.05690.0221-0.1180.04390.17540.04190.07030.0776-0.0523-0.04370.22130.02370.0633-40.0791-9.549337.4432
40.2802-0.1126-0.59630.514-0.1892.75860.1082-0.05680.0954-0.1412-0.0745-0.0345-0.2418-0.0578-0.03370.11290.0111-0.00490.0982-0.05590.0764-16.407417.704919.4939
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A134 - 480
2X-RAY DIFFRACTION2B133 - 480
3X-RAY DIFFRACTION3C135 - 479
4X-RAY DIFFRACTION4D134 - 479

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