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- PDB-1xo2: Crystal structure of a human cyclin-dependent kinase 6 complex wi... -

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Basic information

Entry
Database: PDB / ID: 1xo2
TitleCrystal structure of a human cyclin-dependent kinase 6 complex with a flavonol inhibitor, fisetin
Components
  • Cell division protein kinase 6
  • Cyclin
KeywordsCELL CYCLE/TRANSFERASE / human cyclin-dependent kinase 6 / fisetin / CELL CYCLE-TRANSFERASE COMPLEX
Function / homology
Function and homology information


cyclin D2-CDK6 complex / cyclin D3-CDK6 complex / cyclin D1-CDK6 complex / cell dedifferentiation / Evasion of Oncogene Induced Senescence Due to Defective p16INK4A binding to CDK4 and CDK6 / Evasion of Oxidative Stress Induced Senescence Due to Defective p16INK4A binding to CDK4 and CDK6 / Drug-mediated inhibition of CDK4/CDK6 activity / FBXO family protein binding / lateral ventricle development / symbiont-mediated perturbation of host cell cycle progression ...cyclin D2-CDK6 complex / cyclin D3-CDK6 complex / cyclin D1-CDK6 complex / cell dedifferentiation / Evasion of Oncogene Induced Senescence Due to Defective p16INK4A binding to CDK4 and CDK6 / Evasion of Oxidative Stress Induced Senescence Due to Defective p16INK4A binding to CDK4 and CDK6 / Drug-mediated inhibition of CDK4/CDK6 activity / FBXO family protein binding / lateral ventricle development / symbiont-mediated perturbation of host cell cycle progression / negative regulation of myeloid cell differentiation / type B pancreatic cell development / negative regulation of monocyte differentiation / astrocyte development / dentate gyrus development / regulation of cell motility / gliogenesis / Regulation of RUNX1 Expression and Activity / regulation of hematopoietic stem cell differentiation / positive regulation of cell-matrix adhesion / generation of neurons / Defective binding of RB1 mutants to E2F1,(E2F2, E2F3) / negative regulation of cell cycle / negative regulation of cellular senescence / negative regulation of cell differentiation / hematopoietic stem cell differentiation / negative regulation of osteoblast differentiation / cyclin-dependent kinase / cyclin-dependent protein serine/threonine kinase activity / cyclin-dependent protein kinase holoenzyme complex / regulation of G2/M transition of mitotic cell cycle / ruffle / Notch signaling pathway / cyclin binding / regulation of erythrocyte differentiation / G1/S transition of mitotic cell cycle / Oncogene Induced Senescence / response to virus / positive regulation of fibroblast proliferation / negative regulation of epithelial cell proliferation / Cyclin D associated events in G1 / T cell differentiation in thymus / regulation of gene expression / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / regulation of cell cycle / negative regulation of cell population proliferation / cell division / protein serine kinase activity / DNA damage response / centrosome / positive regulation of gene expression / negative regulation of transcription by RNA polymerase II / signal transduction / nucleoplasm / ATP binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Cyclin domain, herpesvirus / Herpesviridae viral cyclin / Cyclin, herpesvirus / Cyclin-dependent kinase 6 / : / Cyclins signature. / Cyclin / Cyclin-like / Cyclin A; domain 1 / Cyclin, N-terminal ...Cyclin domain, herpesvirus / Herpesviridae viral cyclin / Cyclin, herpesvirus / Cyclin-dependent kinase 6 / : / Cyclins signature. / Cyclin / Cyclin-like / Cyclin A; domain 1 / Cyclin, N-terminal / Cyclin, N-terminal domain / Cyclin-like / domain present in cyclins, TFIIB and Retinoblastoma / Cyclin-like superfamily / : / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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
3,7,3',4'-TETRAHYDROXYFLAVONE / Cyclin-dependent kinase 6 / Cyclin homolog
Similarity search - Component
Biological speciesSaimiriine herpesvirus 2 (Herpesvirus saimiri)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsLu, H.S. / Chang, D.J. / Baratte, B. / Meijer, L. / Schulze-Gahmen, U.
CitationJournal: J.Med.Chem. / Year: 2005
Title: Crystal Structure of a Human Cyclin-Dependent Kinase 6 Complex with a Flavonol Inhibitor, Fisetin.
Authors: Lu, H.S. / Chang, D.J. / Baratte, B. / Meijer, L. / Schulze-Gahmen, U.
History
DepositionOct 5, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 1, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Cyclin
B: Cell division protein kinase 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,0183
Polymers63,7322
Non-polymers2861
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4880 Å2
ΔGint-20 kcal/mol
Surface area22510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.162, 66.162, 448.596
Angle α, β, γ (deg.)90, 90, 120
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Cyclin / V-cyclin


Mass: 28665.416 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saimiriine herpesvirus 2 (Herpesvirus saimiri)
Genus: Rhadinovirus / Gene: 72, ECLF2 / Plasmid: pFASTBacHTa / Cell line (production host): sf-9 / Production host: Escherichia coli (E. coli) / References: UniProt: Q01043
#2: Protein Cell division protein kinase 6 / Serine/threonine-protein kinase PLSTIRE


Mass: 35066.332 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDK6 / Plasmid: pFASTBac1 / Cell line (production host): sf-9 / Production host: Escherichia coli (E. coli) / References: UniProt: Q00534, EC: 2.7.1.37
#3: Chemical ChemComp-FSE / 3,7,3',4'-TETRAHYDROXYFLAVONE / Fisetin / 2-(3,4-DIHYDROXYPHENYL)-3,7-DIHYDROXY-4H-CHROMEN-4-ONE


Mass: 286.236 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H10O6

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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: 2.5 Å3/Da / Density % sol: 51 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
DetectorDetector: CCD / Date: Feb 23, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 14353 / % possible obs: 91.5 % / Redundancy: 8.16 % / Biso Wilson estimate: 50 Å2 / Rmerge(I) obs: 0.122 / Net I/σ(I): 18.3
Reflection shellResolution: 2.8→2.88 Å / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 3.1 / Num. unique all: 1154 / % possible all: 90.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
TRUNCATEdata reduction
AMoREphasing
CNSrefinement
HKL-2000data reduction
CCP4(TRUNCATE)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JOW

1jow


Resolution: 2.9→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.313 952 7.5 %RANDOM
Rwork0.26 ---
obs-12984 91.4 %-
Refinement stepCycle: LAST / Resolution: 2.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4151 0 21 0 4172
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.008
X-RAY DIFFRACTIONo_bond_d_na
X-RAY DIFFRACTIONo_bond_d_prot
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_d_na
X-RAY DIFFRACTIONo_angle_d_prot
X-RAY DIFFRACTIONo_angle_deg1.38
X-RAY DIFFRACTIONo_angle_deg_na
X-RAY DIFFRACTIONo_angle_deg_prot
X-RAY DIFFRACTIONo_dihedral_angle_d
X-RAY DIFFRACTIONo_dihedral_angle_d_na
X-RAY DIFFRACTIONo_dihedral_angle_d_prot
X-RAY DIFFRACTIONo_improper_angle_d
X-RAY DIFFRACTIONo_improper_angle_d_na
X-RAY DIFFRACTIONo_improper_angle_d_prot
X-RAY DIFFRACTIONo_mcbond_it
X-RAY DIFFRACTIONo_mcangle_it
X-RAY DIFFRACTIONo_scbond_it
X-RAY DIFFRACTIONo_scangle_it

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