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- PDB-7kxw: Crystal structure of DCLK1-KD in complex with DCLK1-IN-1 -

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Basic information

Entry
Database: PDB / ID: 7kxw
TitleCrystal structure of DCLK1-KD in complex with DCLK1-IN-1
Components(Serine/threonine-protein kinase ...) x 2
KeywordsTRANSFERASE / KINASE / DOUBLECORTIN-LIKE
Function / homology
Function and homology information


axon extension / endosomal transport / protein localization to nucleus / central nervous system development / response to virus / nervous system development / protein phosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction ...axon extension / endosomal transport / protein localization to nucleus / central nervous system development / response to virus / nervous system development / protein phosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding / plasma membrane / cytoplasm
Similarity search - Function
Doublecortin / Doublecortin domain profile. / Domain in the Doublecortin (DCX) gene product / Doublecortin domain / Doublecortin domain superfamily / 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 ...Doublecortin / Doublecortin domain profile. / Domain in the Doublecortin (DCX) gene product / Doublecortin domain / Doublecortin domain superfamily / 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 / Chem-XBD / Serine/threonine-protein kinase DCLK1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.002 Å
AuthorsPatel, O. / Lucet, I.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)APP1162058 Australia
CitationJournal: Commun Biol / Year: 2021
Title: Structural basis for small molecule targeting of Doublecortin Like Kinase 1 with DCLK1-IN-1.
Authors: Patel, O. / Roy, M.J. / Kropp, A. / Hardy, J.M. / Dai, W. / Lucet, I.S.
History
DepositionDec 5, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 22, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 13, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine/threonine-protein kinase DCLK1
B: Serine/threonine-protein kinase DCLK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,0356
Polymers62,6792
Non-polymers1,3554
Water724
1
A: Serine/threonine-protein kinase DCLK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0133
Polymers31,3801
Non-polymers6342
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Serine/threonine-protein kinase DCLK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0223
Polymers31,3001
Non-polymers7222
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)143.950, 61.714, 65.312
Angle α, β, γ (deg.)90.000, 103.040, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 383 through 390 or resid 392...
21(chain B and (resid 383 through 390 or resid 392...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 383 through 390 or resid 392...A383 - 390
121(chain A and (resid 383 through 390 or resid 392...A392 - 393
131(chain A and (resid 383 through 390 or resid 392...A394
141(chain A and (resid 383 through 390 or resid 392...A382 - 3
151(chain A and (resid 383 through 390 or resid 392...A382 - 3
161(chain A and (resid 383 through 390 or resid 392...A382 - 3
171(chain A and (resid 383 through 390 or resid 392...A382 - 3
211(chain B and (resid 383 through 390 or resid 392...B383 - 390
221(chain B and (resid 383 through 390 or resid 392...B392 - 396
231(chain B and (resid 383 through 390 or resid 392...B402 - 404
241(chain B and (resid 383 through 390 or resid 392...B405
251(chain B and (resid 383 through 390 or resid 392...B382 - 3
261(chain B and (resid 383 through 390 or resid 392...B382 - 3
271(chain B and (resid 383 through 390 or resid 392...B382 - 3
281(chain B and (resid 383 through 390 or resid 392...B382 - 3

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Components

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Serine/threonine-protein kinase ... , 2 types, 2 molecules AB

#1: Protein Serine/threonine-protein kinase DCLK1 / Doublecortin domain-containing protein 3A / Doublecortin-like and CAM kinase-like 1 / Doublecortin- ...Doublecortin domain-containing protein 3A / Doublecortin-like and CAM kinase-like 1 / Doublecortin-like kinase 1


Mass: 31379.725 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DCLK1, DCAMKL1, DCDC3A, KIAA0369 / Plasmid: pCOLD / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: O15075, non-specific serine/threonine protein kinase
#2: Protein Serine/threonine-protein kinase DCLK1 / Doublecortin domain-containing protein 3A / Doublecortin-like and CAM kinase-like 1 / Doublecortin- ...Doublecortin domain-containing protein 3A / Doublecortin-like and CAM kinase-like 1 / Doublecortin-like kinase 1


Mass: 31299.744 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DCLK1, DCAMKL1, DCDC3A, KIAA0369 / Plasmid: pCOLD / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: O15075, non-specific serine/threonine protein kinase

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Non-polymers , 4 types, 8 molecules

#3: Chemical ChemComp-XBD / 2-{[2-methoxy-4-(4-methylpiperazin-1-yl)phenyl]amino}-11-methyl-5-(2,2,2-trifluoroethyl)-5,11-dihydro-6H-pyrimido[4,5-b][1,4]benzodiazepin-6-one


Mass: 527.541 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C26H28F3N7O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 2.25 Å3/Da / Density % sol: 45.37 % / Mosaicity: 0.31 °
Crystal growTemperature: 298 K / Method: evaporation / pH: 7.25 / Details: PEG400, ammonium sulfphate, Hepes

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 21, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 3→44.29 Å / Num. obs: 11200 / % possible obs: 98.8 % / Redundancy: 6.8 % / Biso Wilson estimate: 62.43 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.156 / Rpim(I) all: 0.064 / Rrim(I) all: 0.169 / Net I/σ(I): 11.4 / Num. measured all: 76277
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
3-3.186.80.7751133716690.8190.3160.8393.693
9.01-44.296.70.05729424390.9970.0230.06225.699.2

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Processing

Software
NameVersionClassification
Aimless0.5.32data scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.27data extraction
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JZJ

5jzj


Resolution: 3.002→44.288 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 27.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2597 566 5.06 %
Rwork0.2 10623 -
obs0.2031 11189 98.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 114.52 Å2 / Biso mean: 56.8085 Å2 / Biso min: 24.83 Å2
Refinement stepCycle: final / Resolution: 3.002→44.288 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3935 0 96 4 4035
Biso mean--66.28 39.81 -
Num. residues----506
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1458X-RAY DIFFRACTION2.109TORSIONAL
12B1458X-RAY DIFFRACTION2.109TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.002-3.3040.33811280.2439253095
3.304-3.78190.27581450.20962666100
3.7819-4.76380.25241600.18162670100
4.7638-44.2880.23161330.19592757100

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