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- PDB-7kx8: Crystal structure of DCLK1-Cter in complex with FMF-03-055-1 -

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Basic information

Entry
Database: PDB / ID: 7kx8
TitleCrystal structure of DCLK1-Cter in complex with FMF-03-055-1
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-X8J / Serine/threonine-protein kinase DCLK1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 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 ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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

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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)71,1494
Polymers70,2022
Non-polymers9472
Water00
1
A: Serine/threonine-protein kinase DCLK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5752
Polymers35,1011
Non-polymers4741
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Serine/threonine-protein kinase DCLK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5752
Polymers35,1011
Non-polymers4741
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.920, 62.430, 72.080
Angle α, β, γ (deg.)90.000, 96.070, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 382 through 387 or (resid 388...
21(chain B and (resid 382 through 427 or (resid 430...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ILEILETHRTHR(chain A and (resid 382 through 387 or (resid 388...AA382 - 38713 - 18
12GLUGLUGLUGLU(chain A and (resid 382 through 387 or (resid 388...AA38819
13ILEILEPHEPHE(chain A and (resid 382 through 387 or (resid 388...AA382 - 67013 - 300
14ILEILEPHEPHE(chain A and (resid 382 through 387 or (resid 388...AA382 - 67013 - 300
15ILEILEPHEPHE(chain A and (resid 382 through 387 or (resid 388...AA382 - 67013 - 300
16ILEILEPHEPHE(chain A and (resid 382 through 387 or (resid 388...AA382 - 67013 - 300
21ILEILEARGARG(chain B and (resid 382 through 427 or (resid 430...BB382 - 42713 - 58
22GLUGLUMETMET(chain B and (resid 382 through 427 or (resid 430...BB430 - 43261 - 63
23PHEPHEVALVAL(chain B and (resid 382 through 427 or (resid 430...BB380 - 64711 - 278
24PHEPHEVALVAL(chain B and (resid 382 through 427 or (resid 430...BB380 - 64711 - 278
25PHEPHEVALVAL(chain B and (resid 382 through 427 or (resid 430...BB380 - 64711 - 278
26PHEPHEVALVAL(chain B and (resid 382 through 427 or (resid 430...BB380 - 64711 - 278

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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: 35100.988 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-X8J / 5-ethyl-2-{[2-methoxy-4-(4-methylpiperazin-1-yl)phenyl]amino}-11-methyl-5,11-dihydro-6H-pyrimido[4,5-b][1,4]benzodiazepin-6-one


Mass: 473.570 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H31N7O2 / Feature type: SUBJECT OF INVESTIGATION
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: 2.1 Å3/Da / Density % sol: 41.45 % / Mosaicity: 1.31 °
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: 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: 3.1→71.68 Å / Num. obs: 10702 / % possible obs: 99.5 % / Redundancy: 4.7 % / Biso Wilson estimate: 46.34 Å2 / CC1/2: 0.98 / Rmerge(I) obs: 0.236 / Rpim(I) all: 0.115 / Rrim(I) all: 0.263 / Net I/σ(I): 7.3 / Num. measured all: 50639 / Scaling rejects: 18
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
3.1-3.314.80.927928219260.7090.4441.0322.699.8
8.77-71.684.70.05523885120.9980.0260.06116.999.7

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Processing

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

5jzj


Resolution: 3.1→71.676 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2509 560 5.24 %
Rwork0.1925 10133 -
obs0.1957 10693 99.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 96.42 Å2 / Biso mean: 40.8174 Å2 / Biso min: 7.8 Å2
Refinement stepCycle: final / Resolution: 3.1→71.676 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3921 0 70 0 3991
Biso mean--44.1 --
Num. residues----514
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034074
X-RAY DIFFRACTIONf_angle_d0.6585548
X-RAY DIFFRACTIONf_chiral_restr0.047656
X-RAY DIFFRACTIONf_plane_restr0.006736
X-RAY DIFFRACTIONf_dihedral_angle_d5.7252444
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2132X-RAY DIFFRACTION8.055TORSIONAL
12B2132X-RAY DIFFRACTION8.055TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.1003-3.41230.29291360.2382522100
3.4123-3.9060.24121490.19652510100
3.906-4.9210.23491320.1653252199
4.921-71.6760.25171430.1923258099

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