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- PDB-5jzn: Crystal structure of DCLK1-KD in complex with NVP-TAE684 -

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Basic information

Entry
Database: PDB / ID: 5jzn
TitleCrystal structure of DCLK1-KD in complex with NVP-TAE684
ComponentsSerine/threonine-protein kinase DCLK1
KeywordsTRANSFERASE / kinase / doublecortin
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 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site ...Doublecortin / Doublecortin domain profile. / Domain in the Doublecortin (DCX) gene product / Doublecortin domain / Doublecortin domain superfamily / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; 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-GUI / Serine/threonine-protein kinase DCLK1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.85 Å
AuthorsPatel, O. / Lucet, I.
CitationJournal: Structure / Year: 2016
Title: Biochemical and Structural Insights into Doublecortin-like Kinase Domain 1.
Authors: Patel, O. / Dai, W. / Mentzel, M. / Griffin, M.D. / Serindoux, J. / Gay, Y. / Fischer, S. / Sterle, S. / Kropp, A. / Burns, C.J. / Ernst, M. / Buchert, M. / Lucet, I.S.
History
DepositionMay 17, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 24, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2017Group: Data collection / Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / diffrn_source / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _citation.journal_id_ISSN ..._citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Sep 27, 2023Group: 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

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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)63,9245
Polymers62,5992
Non-polymers1,3243
Water84747
1
A: Serine/threonine-protein kinase DCLK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0103
Polymers31,3001
Non-polymers7102
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Serine/threonine-protein kinase DCLK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9142
Polymers31,3001
Non-polymers6141
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)106.360, 106.360, 157.370
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / End auth comp-ID: ASN / End label comp-ID: ASN

Dom-IDBeg auth comp-IDBeg label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1GLYGLYchain AAA379 - 64810 - 279
2PHEPHEchain BBB380 - 64811 - 279

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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 / Fragment: UNP residues 372-649
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 (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: O15075, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-GUI / 5-CHLORO-N-[2-METHOXY-4-[4-(4-METHYLPIPERAZIN-1-YL)PIPERIDIN-1-YL]PHENYL]-N'-(2-PROPAN-2-YLSULFONYLPHENYL)PYRIMIDINE-2,4-DIAMINE / 4-[1-(4-{[5-CHLORO-4-({2-[(1-METHYLETHYL)SULFONYL]PHENYL}AMINO)PYRIMIDIN-2-YL]AMINO}-3-METHOXYPHENYL)PIPERIDIN-4-YL]-1-METHYLPIPERAZIN-1-IUM


Mass: 614.202 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C30H40ClN7O3S
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / Source method: isolated from a natural source / Formula: H2O

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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: 3.83 Å3/Da / Density % sol: 67.89 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 7.5 / Details: PEG400, Hepes

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 21, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.85→59.83 Å / Num. obs: 23585 / % possible obs: 100 % / Redundancy: 5.4 % / Biso Wilson estimate: 45.21 Å2 / CC1/2: 0.982 / Rmerge(I) obs: 0.195 / Rpim(I) all: 0.092 / Rrim(I) all: 0.216 / Net I/σ(I): 7.3 / Num. measured all: 126565 / Scaling rejects: 23
Reflection shell

Diffraction-ID: 1 / Redundancy: 5.5 % / Rejects: _

Resolution (Å)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.85-30.8451870734190.5510.3960.9342.3100
9.01-59.830.09842427660.990.0460.10815.599.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimless0.5.8data scaling
PHENIX1.9_1692refinement
PDB_EXTRACT3.2data extraction
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JZJ

5jzj


Resolution: 2.85→53.18 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 21.66
RfactorNum. reflection% reflection
Rfree0.2248 1194 5.07 %
Rwork0.181 --
obs0.1831 23549 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 102.32 Å2 / Biso mean: 39.2273 Å2 / Biso min: 10.81 Å2
Refinement stepCycle: final / Resolution: 2.85→53.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4108 0 89 47 4244
Biso mean--48.67 31.18 -
Num. residues----534
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084288
X-RAY DIFFRACTIONf_angle_d1.4555844
X-RAY DIFFRACTIONf_chiral_restr0.067685
X-RAY DIFFRACTIONf_plane_restr0.006727
X-RAY DIFFRACTIONf_dihedral_angle_d15.9071548
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2380X-RAY DIFFRACTION4.811TORSIONAL
12B2380X-RAY DIFFRACTION4.811TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.8503-2.96440.36421340.27624832617
2.9644-3.09930.27471320.240524592591
3.0993-3.26270.29351490.225424632612
3.2627-3.46710.27741180.202624962614
3.4671-3.73470.24071290.179524822611
3.7347-4.11040.19691340.15824792613
4.1104-4.70490.16211410.140824632604
4.7049-5.92640.2151310.167425142645
5.9264-53.18920.18691260.167625162642

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