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- PDB-3d5x: Crystal structure of an activated (Thr->Asp) Polo-like kinase 1 (... -

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Basic information

Entry
Database: PDB / ID: 3d5x
TitleCrystal structure of an activated (Thr->Asp) Polo-like kinase 1 (Plk1) catalytic domain in complex with wortmannin.
ComponentsPolo-like kinase 1PLK1
KeywordsTRANSFERASE / Polo-like kinase 1 / Plk1 / catalytic domain / small-molecule inhibitor / Kinase
Function / homology
Function and homology information


polo kinase / mitotic spindle organization / kinetochore / spindle pole / retina development in camera-type eye / mitotic cell cycle / midbody / cell division / phosphorylation / protein serine/threonine kinase activity ...polo kinase / mitotic spindle organization / kinetochore / spindle pole / retina development in camera-type eye / mitotic cell cycle / midbody / cell division / phosphorylation / protein serine/threonine kinase activity / centrosome / ATP binding / nucleus / cytoplasm
Similarity search - Function
Polo-like kinase 1, catalytic domain / Second polo-box domain / First polo-box domain / POLO box domain superfamily / POLO box duplicated region / POLO box domain / POLO box domain profile. / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 ...Polo-like kinase 1, catalytic domain / Second polo-box domain / First polo-box domain / POLO box domain superfamily / POLO box duplicated region / POLO box domain / POLO box domain profile. / 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-KWT / Serine/threonine-protein kinase PLK
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsElling, R.A. / Fucini, R.V. / Romanowski, M.J.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2008
Title: Structures of the wild-type and activated catalytic domains of Brachydanio rerio Polo-like kinase 1 (Plk1): changes in the active-site conformation and interactions with ligands.
Authors: Elling, R.A. / Fucini, R.V. / Romanowski, M.J.
History
DepositionMay 17, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / entity / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / struct_site
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Aug 30, 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

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Assembly

Deposited unit
A: Polo-like kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8712
Polymers34,4421
Non-polymers4281
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)135.542, 135.542, 135.542
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23

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Components

#1: Protein Polo-like kinase 1 / PLK1


Mass: 34442.113 Da / Num. of mol.: 1 / Fragment: catalytic domain / Mutation: T196D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: plk1 / Plasmid: pGEX6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Star / References: UniProt: Q4KMI8, polo kinase
#2: Chemical ChemComp-KWT / (1S,6BR,9AS,11R,11BR)-9A,11B-DIMETHYL-1-[(METHYLOXY)METHYL]-3,6,9-TRIOXO-1,6,6B,7,8,9,9A,10,11,11B-DECAHYDRO-3H-FURO[4, 3,2-DE]INDENO[4,5-H][2]BENZOPYRAN-11-YL ACETATE / [1S-(1A,6BA,9AB,11A,11BB)]-11-(ACETYLOXY)-1,6B,7,8,9A,10,11,11B-OCTAHYDRO-1-(METHOXYMETHLY) -9A,11B-DIMETHYL-3H-FURO[4,3,2-DE]INDENL[4,5-H]-2-BENZOPYRAN-3,6,9,TRIONE / WORTMANNIN / Wortmannin


Mass: 428.432 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H24O8 / Comment: inhibitor*YM

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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: 3.01 Å3/Da / Density % sol: 59.17 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: hanging-drop vapor diffusion at 4 C (277K); protein and wortmannin at a 1:1 molar ratio; protein at 7 mg/ml in 50 mM Tris-HCl pH 7.5, 200 mM NaCl and 3 mM DTT; crystallization condition: 0.1 ...Details: hanging-drop vapor diffusion at 4 C (277K); protein and wortmannin at a 1:1 molar ratio; protein at 7 mg/ml in 50 mM Tris-HCl pH 7.5, 200 mM NaCl and 3 mM DTT; crystallization condition: 0.1 M HEPES pH 7.5, 0.2 M (NH4)2SO4, 22.5% PEG 3350 and 15% glycerol; cryoprotectant: 15% ethylene glycol, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 180 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 25, 2007
RadiationMonochromator: Side-scattering cube root I-beam bent single crystal; asymmetric cut 12.2 degs.
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. obs: 12803 / % possible obs: 99.4 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 10.6
Reflection shellResolution: 2.6→2.74 Å / Rmerge(I) obs: 0.442 / Mean I/σ(I) obs: 2.1 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
CrystalCleardata collection
CrystalCleardata reduction
d*TREKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3d5u

3d5u


Resolution: 2.8→30 Å / Cor.coef. Fo:Fc: 0.902 / Cor.coef. Fo:Fc free: 0.857 / SU B: 15.364 / SU ML: 0.315 / Cross valid method: THROUGHOUT / ESU R: 1.376 / ESU R Free: 0.415 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.29926 720 7 %RANDOM
Rwork0.26041 ---
obs0.2631 9568 99.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 56.496 Å2
Refinement stepCycle: LAST / Resolution: 2.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2196 0 31 0 2227
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0222280
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0261.9923095
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.8625276
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.64823100
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.39615382
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.3811518
X-RAY DIFFRACTIONr_chiral_restr0.0610.2347
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.021719
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1780.2955
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2960.21578
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1170.256
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1170.230
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0660.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.242.51433
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.14652255
X-RAY DIFFRACTIONr_scbond_it0.9082.5965
X-RAY DIFFRACTIONr_scangle_it1.4865840
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.801→2.898 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.337 64 -
Rwork0.327 928 -
obs--99.5 %

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