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- PDB-7kx6: Crystal structure of DCLK1-KD in complex with XMD8-85 -

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Basic information

Entry
Database: PDB / ID: 7kx6
TitleCrystal structure of DCLK1-KD in complex with XMD8-85
ComponentsSerine/threonine-protein kinase DCLK1
KeywordsTRANSFERASE / KINASE / DOUBLECORTIN-LIKE
Function / homology
Function and homology information


central nervous system projection neuron axonogenesis / axon extension / negative regulation of protein localization to nucleus / dendrite morphogenesis / endosomal transport / protein localization to nucleus / forebrain development / neuron projection morphogenesis / central nervous system development / neuron migration ...central nervous system projection neuron axonogenesis / axon extension / negative regulation of protein localization to nucleus / dendrite morphogenesis / endosomal transport / protein localization to nucleus / forebrain development / neuron projection morphogenesis / central nervous system development / neuron migration / response to virus / nervous system development / postsynaptic density / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding / plasma membrane
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
Chem-X7Y / Serine/threonine-protein kinase DCLK1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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 3, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 22, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 27, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)63,5194
Polymers62,5992
Non-polymers9192
Water1,65792
1
A: Serine/threonine-protein kinase DCLK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7592
Polymers31,3001
Non-polymers4601
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)31,7592
Polymers31,3001
Non-polymers4601
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.180, 63.330, 152.491
Angle α, β, γ (deg.)90.000, 100.470, 90.000
Int Tables number5
Space group name H-MI121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 382 through 441 or (resid 442...
21(chain B and (resid 382 through 398 or (resid 401...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 382 through 441 or (resid 442...A382 - 441
121(chain A and (resid 382 through 441 or (resid 442...A442
211(chain B and (resid 382 through 398 or (resid 401...B382 - 398
221(chain B and (resid 382 through 398 or (resid 401...B401 - 402
231(chain B and (resid 382 through 398 or (resid 401...B382 - 1
241(chain B and (resid 382 through 398 or (resid 401...B382 - 1
251(chain B and (resid 382 through 398 or (resid 401...B382 - 1
261(chain B and (resid 382 through 398 or (resid 401...B382 - 1

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Components

#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: 31299.744 Da / Num. of mol.: 2
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: Chemical ChemComp-X7Y / 2-{[2-methoxy-4-(4-methylpiperazin-1-yl)phenyl]amino}-5,11-dimethyl-5,11-dihydro-6H-pyrimido[4,5-b][1,4]benzodiazepin-6-one


Mass: 459.543 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H29N7O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.51 Å3/Da / Density % sol: 50.99 % / Mosaicity: 1.37 °
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: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.5→74.98 Å / Num. obs: 21500 / % possible obs: 99.1 % / Redundancy: 4.7 % / Biso Wilson estimate: 33.32 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.117 / Rpim(I) all: 0.06 / Rrim(I) all: 0.132 / Net I/σ(I): 10.8 / Num. measured all: 101629 / Scaling rejects: 42
Reflection shell

Diffraction-ID: 1 / % possible all: 99.7

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs
2.5-2.64.80.6741176724360.7020.3450.762.9
9.01-74.984.70.03823144970.9990.0190.04325.1

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
Aimless0.5.8data scaling
PDB_EXTRACT3.27data extraction
Cootmodel building
Blu-Icedata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JZJ

5jzj


Resolution: 2.5→56.093 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2251 1063 4.95 %
Rwork0.1924 20432 -
obs0.1941 21495 99.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 91.08 Å2 / Biso mean: 37.7305 Å2 / Biso min: 11.4 Å2
Refinement stepCycle: final / Resolution: 2.5→56.093 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3923 0 68 92 4083
Biso mean--37.81 30.99 -
Num. residues----512
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044080
X-RAY DIFFRACTIONf_angle_d0.7075562
X-RAY DIFFRACTIONf_chiral_restr0.068657
X-RAY DIFFRACTIONf_plane_restr0.005742
X-RAY DIFFRACTIONf_dihedral_angle_d6.6142455
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2245X-RAY DIFFRACTION9.257TORSIONAL
12B2245X-RAY DIFFRACTION9.257TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.5001-2.61380.31061320.24412578100
2.6138-2.75160.28911340.2273252399
2.7516-2.9240.2521270.2123252999
2.924-3.14980.27721290.2229255399
3.1498-3.46670.23851200.2028258299
3.4667-3.96820.20091470.1787252699
3.9682-4.99910.17311210.153255498
4.9991-56.0930.21331530.1876258798

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