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- PDB-4crs: Human Protein Kinase N2 (PKN2, PRKCL2) in complex with ATPgammaS -

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Basic information

Entry
Database: PDB / ID: 4crs
TitleHuman Protein Kinase N2 (PKN2, PRKCL2) in complex with ATPgammaS
ComponentsSERINE/THREONINE-PROTEIN KINASE N2
KeywordsTRANSFERASE / PRKCL2 / PKN2 / AGC
Function / homology
Function and homology information


epithelial cell migration / protein kinase C / diacylglycerol-dependent serine/threonine kinase activity / cell projection organization / apical junction assembly / regulation of cell motility / RNA polymerase binding / intermediate filament cytoskeleton / apical junction complex / RHOB GTPase cycle ...epithelial cell migration / protein kinase C / diacylglycerol-dependent serine/threonine kinase activity / cell projection organization / apical junction assembly / regulation of cell motility / RNA polymerase binding / intermediate filament cytoskeleton / apical junction complex / RHOB GTPase cycle / RHOC GTPase cycle / positive regulation of cytokinesis / cleavage furrow / RHOA GTPase cycle / positive regulation of viral genome replication / RHO GTPases activate PKNs / RAC1 GTPase cycle / positive regulation of mitotic cell cycle / small GTPase binding / histone deacetylase binding / lamellipodium / kinase activity / midbody / nuclear body / cell adhesion / protein kinase activity / intracellular signal transduction / cadherin binding / cell cycle / cell division / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / apoptotic process / perinuclear region of cytoplasm / signal transduction / protein-containing complex / RNA binding / nucleoplasm / ATP binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Serine/threonine-protein kinase N, first HR1 domain / Serine/threonine-protein kinase N, C2 domain / Hr1 repeat / Rho effector or protein kinase C-related kinase homology region 1 homologues / HR1 repeat superfamily / HR1 rho-binding domain / REM-1 domain profile. / Protein kinase, C-terminal / Protein kinase C terminal domain / Protein kinase C conserved region 2 (CalB) ...Serine/threonine-protein kinase N, first HR1 domain / Serine/threonine-protein kinase N, C2 domain / Hr1 repeat / Rho effector or protein kinase C-related kinase homology region 1 homologues / HR1 repeat superfamily / HR1 rho-binding domain / REM-1 domain profile. / Protein kinase, C-terminal / Protein kinase C terminal domain / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain profile. / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / C2 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
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / Serine/threonine-protein kinase N2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsMathea, S. / Elkins, J.M. / Shrestha, L. / Szklarz, M. / Tallant, C. / Newman, J.A. / Cooper, C.D. / Shrestha, B. / Tumber, A. / Cocking, R. ...Mathea, S. / Elkins, J.M. / Shrestha, L. / Szklarz, M. / Tallant, C. / Newman, J.A. / Cooper, C.D. / Shrestha, B. / Tumber, A. / Cocking, R. / Salah, E. / von Delft, F. / Arrowsmith, C. / Edwards, A.M. / Bountra, C. / Knapp, S.
CitationJournal: To be Published
Title: Structure of Pkn2
Authors: Mathea, S. / Knapp, S.
History
DepositionFeb 28, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 12, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_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 N2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,4204
Polymers39,7761
Non-polymers6443
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.639, 68.639, 185.473
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein SERINE/THREONINE-PROTEIN KINASE N2 / PKN GAMMA / PROTEIN KINASE C-LIKE 2 / PROTEIN-KINASE C-RELATED KINASE 2 / PROTEIN KINASE N2


Mass: 39776.102 Da / Num. of mol.: 1 / Fragment: KINASE DOMAIN, RESIDUES 646-984
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PFB-6HZB / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: Q16513, protein kinase C
#2: Chemical ChemComp-AGS / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-GAMMA-S / ADENOSINE 5'-(3-THIOTRIPHOSPHATE) / ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE) / ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE


Mass: 523.247 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O12P3S / Comment: ATP-gamma-S, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4

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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: 3.2 Å3/Da / Density % sol: 61.6 % / Description: NONE
Crystal growpH: 5.8
Details: 2.3M AMMONIUM SULPHATE, 0.1M CITRATE PH 5.8, 0.2M SODIUM/POTASSIUM TARTRATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 18, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.75→61.82 Å / Num. obs: 13681 / % possible obs: 99.2 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 6.2
Reflection shellResolution: 2.75→2.88 Å / Redundancy: 3.5 % / Rmerge(I) obs: 1.2 / Mean I/σ(I) obs: 1.3 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1O6L

1o6l


Resolution: 2.75→61.82 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.925 / SU B: 19.062 / SU ML: 0.342 / Cross valid method: THROUGHOUT / ESU R: 0.749 / ESU R Free: 0.345 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.26201 694 5.2 %RANDOM
Rwork0.2098 ---
obs0.21251 12670 96.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 76.443 Å2
Baniso -1Baniso -2Baniso -3
1-2.41 Å21.21 Å20 Å2
2--2.41 Å20 Å2
3----7.82 Å2
Refinement stepCycle: LAST / Resolution: 2.75→61.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2700 0 37 0 2737
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0192803
X-RAY DIFFRACTIONr_bond_other_d0.0010.022572
X-RAY DIFFRACTIONr_angle_refined_deg1.1881.9833804
X-RAY DIFFRACTIONr_angle_other_deg0.73835920
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7955332
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.5523.431137
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.93515462
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3161521
X-RAY DIFFRACTIONr_chiral_restr0.0620.2407
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213108
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02660
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.0987.5581334
X-RAY DIFFRACTIONr_mcbond_other3.0947.5541333
X-RAY DIFFRACTIONr_mcangle_it5.12211.3261664
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.1617.9511465
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.75→2.822 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.436 55 -
Rwork0.376 737 -
obs--81.23 %

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