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- PDB-8r8e: DYRK1a in Complex with 2-Cyclopentyl-7-iodo-1H-indole-3-carbonitrile -

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Basic information

Entry
Database: PDB / ID: 8r8e
TitleDYRK1a in Complex with 2-Cyclopentyl-7-iodo-1H-indole-3-carbonitrile
Components(Dual specificity tyrosine-phosphorylation-regulated kinase ...) x 2
KeywordsTRANSFERASE / Small Molecule / Kinase / Halogen Bond / Water interaction
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 / : / 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
DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / : / Dual specificity tyrosine-phosphorylation-regulated kinase 1A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.22 Å
AuthorsStahlecker, J. / Dammann, M. / Stehle, T. / Boeckler, F.M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J Chem Theory Comput / Year: 2024
Title: Halogen Bonding on Water─A Drop in the Ocean?
Authors: Engelhardt, M.U. / Zimmermann, M.O. / Dammann, M. / Stahlecker, J. / Poso, A. / Kronenberger, T. / Kunick, C. / Stehle, T. / Boeckler, F.M.
History
DepositionNov 29, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 25, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 1.2Dec 18, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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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)176,13064
Polymers168,2464
Non-polymers7,88460
Water9,332518
1
A: Dual specificity tyrosine-phosphorylation-regulated kinase 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,70821
Polymers42,0821
Non-polymers2,62620
Water181
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)44,18217
Polymers42,0821
Non-polymers2,10016
Water181
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)43,71313
Polymers42,0821
Non-polymers1,63112
Water181
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)43,52813
Polymers42,0021
Non-polymers1,52612
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)244.236, 64.473, 147.332
Angle α, β, γ (deg.)90.000, 115.580, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-671-

HOH

21A-756-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and ((resid 136 and (name N or name...
d_2ens_1(chain "B" and ((resid 136 and (name N or name...
d_3ens_1(chain "C" and (resid 136 through 147 or (resid 148...
d_4ens_1(chain "D" and ((resid 136 and (name N or name...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11TYRTYRGLNGLNAA136 - 32012 - 196
d_12ILEILEALAALAAA322 - 391198 - 267
d_13LYSLYSLYSLYSAA393 - 480269 - 356
d_21TYRTYRGLNGLNBB136 - 32012 - 196
d_22ILEILEALAALABB322 - 391198 - 267
d_23LYSLYSLYSLYSBB393 - 480269 - 356
d_31TYRTYRGLNGLNCC136 - 32012 - 196
d_32ILEILEALAALACC322 - 391198 - 267
d_33LYSLYSLYSLYSCC393 - 480269 - 356
d_41TYRTYRGLNGLNDD136 - 32012 - 196
d_42ILEILEALAALADD322 - 391198 - 267
d_43LYSLYSLYSLYSDD393 - 480269 - 356

NCS oper:
IDCodeMatrixVector
1given(0.875936457963, 0.478769427055, -0.0592887622452), (0.477959141132, -0.877932750836, -0.0280917144115), (-0.0655010001454, -0.00373104906179, -0.997845528252)-17.2724118926, 10.9021019335, 73.8739997236
2given(-0.568556173565, -0.821379919859, 0.0455950079911), (-0.821890499572, 0.569534324803, 0.0112543140071), (-0.0352119896278, -0.0310753941878, -0.998896609096)-25.9576708349, -13.6569336426, 17.0163051891
3given(0.898805262064, -0.436994573619, -0.0344215559443), (-0.435792708691, -0.899272978607, 0.0373205707341), (-0.0472632620375, -0.0185432622568, -0.998710334124)-47.1671058582, 11.3000407406, 59.4316290421

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Components

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Dual specificity tyrosine-phosphorylation-regulated kinase ... , 2 types, 4 molecules ABCD

#1: Protein Dual specificity tyrosine-phosphorylation-regulated kinase 1A / Dual specificity YAK1-related kinase / HP86 / Protein kinase minibrain homolog / hMNB


Mass: 42081.535 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DYRK1A, DYRK, MNB, MNBH / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q13627, dual-specificity kinase
#2: Protein Dual specificity tyrosine-phosphorylation-regulated kinase 1A


Mass: 42001.555 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DYRK1A / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q13627

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Non-polymers , 10 types, 578 molecules

#3: Chemical
ChemComp-YOX / 2-cyclopentyl-7-iodanyl-1~{H}-indole-3-carbonitrile


Mass: 336.171 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H13IN2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Chemical
ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#8: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H8O3
#9: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#10: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 25 / Source method: obtained synthetically / Formula: SO4
#11: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#12: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 518 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.11 Å3/Da / Density % sol: 60.44 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M TRIS (pH = 8.5), 0.1 M Li2SO4, 34 % (v/v) PEG300, 12 mg/ml Protein, Dropsize (resovoir + Protein) 2 + 4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: May 13, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.22→50 Å / Num. obs: 102354 / % possible obs: 99.6 % / Redundancy: 4.54 % / Biso Wilson estimate: 50.72 Å2 / CC1/2: 0.99 / Rrim(I) all: 0.119 / Net I/σ(I): 9.66
Reflection shellResolution: 2.22→2.35 Å / Redundancy: 4.42 % / Mean I/σ(I) obs: 1.07 / Num. unique obs: 16236 / CC1/2: 0.425 / % possible all: 98.6

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.22→49.08 Å / SU ML: 0.3544 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.1077
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2338 1536 1.5 %
Rwork0.1994 100785 -
obs0.1999 102321 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 59.25 Å2
Refinement stepCycle: LAST / Resolution: 2.22→49.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11088 0 454 518 12060
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006711771
X-RAY DIFFRACTIONf_angle_d0.947915870
X-RAY DIFFRACTIONf_chiral_restr0.05781657
X-RAY DIFFRACTIONf_plane_restr0.00761985
X-RAY DIFFRACTIONf_dihedral_angle_d15.84614405
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.921599566542
ens_1d_3AAX-RAY DIFFRACTIONTorsion NCS1.20342987383
ens_1d_4AAX-RAY DIFFRACTIONTorsion NCS0.916288279066
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.22-2.290.38921360.35518924X-RAY DIFFRACTION97.57
2.29-2.370.33871390.30179086X-RAY DIFFRACTION99.92
2.37-2.470.33441390.2929116X-RAY DIFFRACTION99.89
2.47-2.580.29561390.25339152X-RAY DIFFRACTION99.94
2.58-2.720.25991380.23339091X-RAY DIFFRACTION99.94
2.72-2.890.28031400.23149159X-RAY DIFFRACTION99.94
2.89-3.110.2631400.23629183X-RAY DIFFRACTION99.95
3.11-3.420.2431400.20369182X-RAY DIFFRACTION99.96
3.42-3.920.20061400.17299200X-RAY DIFFRACTION99.91
3.92-4.940.19671410.15119255X-RAY DIFFRACTION99.83
4.94-49.080.20311440.18569437X-RAY DIFFRACTION99.65
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)
11.97434483309-0.08757787864940.674302818822.649850977691.178554436372.417928036750.170940912622-0.2394198291640.06704361935460.1896395552010.0295298401268-0.4332186381460.09053809704140.2529028688320.0001986284627640.5613058651720.0007173465710940.005004899931380.407033554193-0.03745131433640.4742947315777.38629.33933.655
21.15747323881.5392944760.2512814196662.00331897540.1926888031371.647644871710.0891604420143-0.123076962573-0.05266341204830.177152521938-0.0192566071834-0.0172762618639-0.0195649192677-0.0482723811061-0.0001634410090.44690525384-0.0115753449731-0.01051813971460.2781364067460.03627777228160.390462758076-2.5616.78223.252
31.41753362977-0.1443816587370.07410894085251.13497914450.1484081378291.811361661120.08892030622540.05791281111970.004109017785870.0564668388474-0.05670059303240.136358206148-0.0567211027646-0.220643542818-3.48132522911E-50.351416010955-0.01080211225590.03123534214020.305239709140.02549268030490.412265399346-11.84117.4437.439
41.2785204472-0.272384522004-0.8980453550872.820578658230.293246947872.169911365220.17980404864-0.04881072830340.2968979870180.02166300890570.0708708952988-0.38704301899-0.2454246057630.04148500803270.0001644520626320.639395666908-0.02931981691420.0844687383710.384093906923-0.0655253700850.5302892283221.62-12.18639.676
52.1402635988-1.334485868150.05590050297780.9608380035380.2930551748571.50952837790.174136192680.08212960404780.117264838211-0.303320000791-0.0507712568323-0.263115063586-0.002290410853310.184438413150.0006464328754580.657397907420.01102757449680.1077713745320.4178521860130.007388271404920.477153899629-12.911-5.84950.833
61.81107436062-0.14505346277-0.005263314101361.838760199030.2317444378632.03617933346-0.012840731534-0.126855777179-0.00212476117336-0.1014907480050.0499451244459-0.05682378602950.05151404214170.1219943072292.63085256914E-50.4314453238760.009045957992290.02766141400720.43299878491-0.008705755887520.370881371473-19.829-10.37567.235
70.688315154839-0.6621459092010.8044316436071.59068076702-0.2117068969961.236080096410.3013828473740.179712194335-0.402824289549-0.0251193339809-0.002369511512070.3627495978380.611575885727-0.2466309778390.0001484819492810.763278300198-0.0969977300767-0.245668209151.03696899712-0.03006930105910.762978254723-52.541-2.472-17.631
82.173303738670.2308929962360.1060739184680.3085637644890.1092782106911.020958448240.3037060684190.3643846494-0.458357907061-0.235364405877-0.1519123800390.3464552814930.331176857737-0.3662379255720.002189042436960.590563088654-0.0960193011715-0.1166955414220.734453566237-0.005896210860290.65712774342-37.015-1.778-6.756
92.451550530250.1147447681480.2497044235891.22689045370.1646339636011.839738087820.0373366955545-0.154915669169-0.08985641130460.126255147839-0.03160799988730.1309543169550.0883309553222-0.369214729357-0.000700326325260.41299841598-0.101835253877-0.03116118178550.5940798404390.09815863861790.490154404173-33.1896.0759.435
101.465542596130.6936583575520.2423914247011.245429941131.110155336091.34995089220.1499910919190.279169807431-0.183161668442-0.22833489019-0.0250566121059-0.337032432296-0.03178073073090.3576562556990.0001661348684890.568867639545-0.0845249906581-0.1092071059551.245118928230.192210162420.606157804665-54.375-17.13325.067
110.604747528086-0.34423734055-0.4746457073891.55808410889-0.2790465571331.10534642161-0.127279144760.4510419947760.111353962852-0.1327531198840.1731046006190.123004203667-0.192573642778-0.00549309538010.000152845989020.483040007359-0.125473237411-0.06605063233980.9435971169620.2016507121090.574838697665-57.439-1.66435.887
121.30041658340.004266151140710.2854054631911.504066205730.3736648252361.91852881724-0.09459573363010.1724843794060.3256082582310.08649367966530.1357119908170.377530683345-0.384299637417-0.404367526474-0.000182251664550.455436387888-0.00689603477779-0.003405012025740.7448846381690.1943629576270.657933066308-65.7750.93352.33
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 135:239 )A135 - 239
2X-RAY DIFFRACTION2( CHAIN A AND RESID 240:320 )A240 - 320
3X-RAY DIFFRACTION3( CHAIN A AND RESID 322:481 )A322 - 481
4X-RAY DIFFRACTION4( CHAIN B AND RESID 135:239 )B135 - 239
5X-RAY DIFFRACTION5( CHAIN B AND RESID 240:320 )B240 - 320
6X-RAY DIFFRACTION6( CHAIN B AND RESID 322:481 )B322 - 481
7X-RAY DIFFRACTION7( CHAIN C AND RESID 136:239 )C136 - 239
8X-RAY DIFFRACTION8( CHAIN C AND RESID 240:320 )C240 - 320
9X-RAY DIFFRACTION9( CHAIN C AND RESID 322:481 )C322 - 481
10X-RAY DIFFRACTION10( CHAIN D AND RESID 135:239 )D135 - 239
11X-RAY DIFFRACTION11( CHAIN D AND RESID 240:320 )D240 - 320
12X-RAY DIFFRACTION12( CHAIN D AND RESID 321:480 )D321 - 480

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