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- PDB-5aik: Human DYRK1A in complex with LDN-211898 -

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Basic information

Entry
Database: PDB / ID: 5aik
TitleHuman DYRK1A in complex with LDN-211898
ComponentsDYRK1A DUAL-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 / : / 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
Chem-AWR / PHOSPHATE ION / Dual specificity tyrosine-phosphorylation-regulated kinase 1A
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsElkins, J.M. / Soundararajan, M. / Muniz, J.R.C. / Cuny, G. / Higgins, J. / Edwards, A. / Bountra, C. / Knapp, S.
CitationJournal: To be published
Title: Dyrk1A with Ldn-211898
Authors: Elkins, J.M. / Soundararajan, M. / Muniz, J.R.C. / Cuny, G. / Higgins, J. / Edwards, A. / Bountra, C. / Knapp, S.
History
DepositionFeb 15, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 25, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 12, 2018Group: Data collection / Database references / Category: citation / Item: _citation.journal_abbrev
Revision 1.2Jul 7, 2021Group: Derived calculations / Other / Refinement description
Category: pdbx_database_status / pdbx_refine_tls_group ...pdbx_database_status / pdbx_refine_tls_group / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_conn / struct_site
Item: _pdbx_database_status.status_code_sf / _pdbx_refine_tls_group.beg_auth_seq_id ..._pdbx_database_status.status_code_sf / _pdbx_refine_tls_group.beg_auth_seq_id / _pdbx_refine_tls_group.end_auth_seq_id / _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 1.3Jan 10, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.4Oct 16, 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: DYRK1A DUAL-SPECIFICITY TYROSINE-PHOSPHORYLATION REGULATED KINASE 1A
B: DYRK1A DUAL-SPECIFICITY TYROSINE-PHOSPHORYLATION REGULATED KINASE 1A
C: DYRK1A DUAL-SPECIFICITY TYROSINE-PHOSPHORYLATION REGULATED KINASE 1A
D: DYRK1A DUAL-SPECIFICITY TYROSINE-PHOSPHORYLATION REGULATED KINASE 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,51218
Polymers178,2134
Non-polymers2,29914
Water1,15364
1
A: DYRK1A DUAL-SPECIFICITY TYROSINE-PHOSPHORYLATION REGULATED KINASE 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0804
Polymers44,5531
Non-polymers5273
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: DYRK1A DUAL-SPECIFICITY TYROSINE-PHOSPHORYLATION REGULATED KINASE 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1755
Polymers44,5531
Non-polymers6224
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: DYRK1A DUAL-SPECIFICITY TYROSINE-PHOSPHORYLATION REGULATED KINASE 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0804
Polymers44,5531
Non-polymers5273
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: DYRK1A DUAL-SPECIFICITY TYROSINE-PHOSPHORYLATION REGULATED KINASE 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1755
Polymers44,5531
Non-polymers6224
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)89.955, 90.891, 232.468
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: _

Dom-IDEns-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA134 - 48131 - 378
21BB134 - 48131 - 378
12AA134 - 48131 - 378
22CC134 - 48131 - 378
13AA134 - 48031 - 377
23DD134 - 48031 - 377
14BB134 - 48131 - 378
24CC134 - 48131 - 378
15BB134 - 48031 - 377
25DD134 - 48031 - 377
16CC134 - 48031 - 377
26DD134 - 48031 - 377

NCS ensembles :
ID
1
2
3
4
5
6

NCS oper:
IDCodeMatrixVector
1given(0.45407, -0.62824, 0.63177), (0.67343, -0.22227, -0.70504), (0.58336, 0.74559, 0.32215)-5.22992, 30.03312, 31.1637
2given(-0.70366, 0.25188, 0.6644), (0.41962, -0.60727, 0.67464), (0.5734, 0.75351, 0.32162)-9.69246, 58.36529, -26.22789
3given(0.22031, -0.97518, -0.02218), (-0.97488, -0.22089, 0.02843), (-0.03263, 0.01536, -0.99935)61.96759, 75.63342, 57.6227

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Components

#1: Protein
DYRK1A DUAL-SPECIFICITY TYROSINE-PHOSPHORYLATION REGULATED KINASE 1A / DUAL SPECIFICITY YAK1-RELATED KINASE / HP86 / PROTEIN KINASE MINIBRAIN HOMOLOG / MNBH / HMNB


Mass: 44553.188 Da / Num. of mol.: 4 / Fragment: KINASE DOMAIN, UNP RESIDUES 128-485
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q13627, non-specific serine/threonine protein kinase
#2: Chemical
ChemComp-AWR / 4-(7-METHOXY-1-(TRIFLUOROMETHYL)-9H-PYRIDO[3,4-B]INDOL-9-yl)butan-1-amine


Mass: 337.340 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H18F3N3O
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / 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: 2.7 Å3/Da / Density % sol: 54 % / Description: NONE
Crystal growpH: 7.5
Details: 0.2M NA/KPO4, 20% PEG 3350, 10% ETHYLENE GLYCOL, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9245
DetectorType: DECTRIS PIXEL / Detector: PIXEL / Date: Jul 9, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9245 Å / Relative weight: 1
ReflectionResolution: 2.7→45.45 Å / Num. obs: 52473 / % possible obs: 98.6 % / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Rmerge(I) obs: 0.18 / Net I/σ(I): 7.4
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 5 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 2.3 / % possible all: 95.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VX3

2vx3


Resolution: 2.7→116.23 Å / Cor.coef. Fo:Fc: 0.903 / Cor.coef. Fo:Fc free: 0.883 / SU B: 31.149 / SU ML: 0.288 / Cross valid method: THROUGHOUT / ESU R: 1.003 / ESU R Free: 0.333 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.25222 2665 5.1 %RANDOM
Rwork0.22681 ---
obs0.22808 49699 98.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.729 Å2
Baniso -1Baniso -2Baniso -3
1-0.67 Å20 Å20 Å2
2---0.66 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.7→116.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11111 0 146 64 11321
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01911519
X-RAY DIFFRACTIONr_bond_other_d0.0060.0210913
X-RAY DIFFRACTIONr_angle_refined_deg1.4431.96615592
X-RAY DIFFRACTIONr_angle_other_deg1.2272.99125054
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.98851366
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.83523.966537
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.699152001
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3651566
X-RAY DIFFRACTIONr_chiral_restr0.210.21658
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02112880
X-RAY DIFFRACTIONr_gen_planes_other0.0060.022714
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_it0.6131.8595488
X-RAY DIFFRACTIONr_mcbond_other0.6131.8595487
X-RAY DIFFRACTIONr_mcangle_it1.1192.7846846
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.5611.9546031
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
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A429820.04
12B429820.04
21A432480.04
22C432480.04
31A431280.05
32D431280.05
41B431420.04
42C431420.04
51B428380.04
52D428380.04
61C430580.05
62D430580.05
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 195 -
Rwork0.327 3599 -
obs--97.71 %
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)
10.90880.1009-0.00972.461-0.3393.72570.0513-0.2774-0.11780.1267-0.102-0.123-0.00210.22090.05060.1154-0.00770.05970.13280.07510.090319.33629.56238.926
21.23990.5028-0.27712.7265-0.10942.63930.01540.0775-0.1008-0.2685-0.12650.03710.1406-0.11290.11110.11940.03370.04070.02530.00330.061113.94724.7949.46
33.360.01160.37813.6782-0.77984.4475-0.0910.1656-0.1995-0.2375-0.1512-0.38990.26060.41040.24230.1530.090.16160.08350.10090.2419.6079.19977.383
41.392-0.096-0.35091.4086-0.46363.071-0.00010.12660.04380.008-0.00160.0668-0.1908-0.16450.00180.140.00680.07060.06860.04120.0777-8.26927.00360.731
51.622-0.1983-0.07255.14460.49932.91760.09860.0457-0.04810.00760.0571-0.1064-0.09840.1484-0.15570.0678-0.00360.02490.0145-0.02760.07519.94474.91719.882
62.34010.2763-0.16941.78760.45041.86-0.02190.4875-0.3162-0.2894-0.30120.4541-0.0413-0.3480.32310.22070.0638-0.10980.2216-0.23310.3031-6.83155.5863.504
72.55731.30160.60132.2411.27722.4187-0.0272-0.08110.064-0.33160.089-0.1415-0.40840.0651-0.06180.24-0.06160.12940.1071-0.00190.141436.42450.96418.647
81.7659-0.1520.47512.3112-0.32133.0237-0.0261-0.62080.02010.21030.2245-0.3454-0.24240.1078-0.19840.1804-0.0620.05860.4659-0.16340.213641.05157.06247.976
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A134 - 241
2X-RAY DIFFRACTION2A242 - 481
3X-RAY DIFFRACTION3B134 - 241
4X-RAY DIFFRACTION4B242 - 481
5X-RAY DIFFRACTION5C134 - 241
6X-RAY DIFFRACTION6C242 - 481
7X-RAY DIFFRACTION7D134 - 241
8X-RAY DIFFRACTION8D242 - 480

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