[English] 日本語
Yorodumi
- PDB-2btr: STRUCTURE OF CDK2 COMPLEXED WITH PNU-198873 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2btr
TitleSTRUCTURE OF CDK2 COMPLEXED WITH PNU-198873
ComponentsCELL DIVISION PROTEIN KINASE 2
KeywordsTRANSFERASE / PROTEIN KINASE / SERINE/THREONINE-PROTEIN 2 KINASE / PHOSPHORYLATION / CELL DIVISION
Function / homology
Function and homology information


Regulation of APC/C activators between G1/S and early anaphase / Regulation of TP53 Activity through Phosphorylation / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / Processing of DNA double-strand break ends / Senescence-Associated Secretory Phenotype (SASP) / SCF(Skp2)-mediated degradation of p27/p21 / Activation of ATR in response to replication stress / G2 Phase / G0 and Early G1 / Regulation of TP53 Degradation ...Regulation of APC/C activators between G1/S and early anaphase / Regulation of TP53 Activity through Phosphorylation / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / Processing of DNA double-strand break ends / Senescence-Associated Secretory Phenotype (SASP) / SCF(Skp2)-mediated degradation of p27/p21 / Activation of ATR in response to replication stress / G2 Phase / G0 and Early G1 / Regulation of TP53 Degradation / DNA Damage/Telomere Stress Induced Senescence / Orc1 removal from chromatin / Activation of the pre-replicative complex / CDK-mediated phosphorylation and removal of Cdc6 / Phosphorylation of proteins involved in G1/S transition by active Cyclin E:Cdk2 complexes / Factors involved in megakaryocyte development and platelet production / Cyclin E associated events during G1/S transition / Cyclin A/B1/B2 associated events during G2/M transition / p53-Dependent G1 DNA Damage Response / Transcriptional regulation of granulopoiesis / Meiotic recombination / Cyclin A:Cdk2-associated events at S phase entry / PTK6 Regulates Cell Cycle / cyclin E1-CDK2 complex / cyclin A1-CDK2 complex / cyclin E2-CDK2 complex / positive regulation of DNA-dependent DNA replication initiation / cyclin A2-CDK2 complex / Y chromosome / cyclin-dependent protein kinase activity / X chromosome / histone phosphorylation / centrosome duplication / centriole replication / cyclin-dependent kinase / cyclin-dependent protein serine/threonine kinase activity / cyclin-dependent protein kinase holoenzyme complex / condensed chromosome / Cajal body / cellular response to nitric oxide / mitotic G1 DNA damage checkpoint / cyclin binding / regulation of gene silencing / potassium ion transport / meiotic cell cycle / chromosome, telomeric region / G1/S transition of mitotic cell cycle / regulation of G2/M transition of mitotic cell cycle / anaphase-promoting complex-dependent catabolic process / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / Ras protein signal transduction / transcription factor complex / G2/M transition of mitotic cell cycle / regulation of signal transduction by p53 class mediator / DNA replication / endosome / peptidyl-serine phosphorylation / centrosome / cell division / DNA repair / protein domain specific binding / protein serine/threonine kinase activity / protein phosphorylation / positive regulation of cell population proliferation / positive regulation of transcription, DNA-templated / negative regulation of transcription by RNA polymerase II / magnesium ion binding / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
Protein kinase-like domain superfamily / Protein kinase, ATP binding site / Protein kinase domain profile. / Serine/Threonine protein kinases active-site signature. / Protein kinases ATP-binding region signature. / Protein kinase domain / Protein kinase domain / Serine/threonine-protein kinase, active site
Cyclin-dependent kinase 2
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.85 Å
AuthorsVulpetti, A. / Casale, E. / Roletto, F. / Amici, R. / Villa, M. / Pevarello, P.
CitationJournal: J.Mol.Graph.Model. / Year: 2006
Title: Structure-Based Drug Design to the Discovery of New 2-Aminothiazole Cdk2 Inhibitors.
Authors: Vulpetti, A. / Casale, E. / Roletto, F. / Amici, R. / Villa, M. / Pevarello, P.
Validation Report
SummaryFull reportAbout validation report
History
DepositionJun 6, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 9, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 3, 2019Group: Data collection / Other / Source and taxonomy
Category: entity_src_gen / pdbx_database_proc / pdbx_database_status
Item: _entity_src_gen.pdbx_host_org_cell_line / _pdbx_database_status.recvd_author_approval

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CELL DIVISION PROTEIN KINASE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2382
Polymers33,9761
Non-polymers2611
Water1,20767
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
γ
α
β
Length a, b, c (Å)53.215, 71.615, 71.588
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein/peptide CELL DIVISION PROTEIN KINASE 2 / / P33 PROTEIN KINASE


Mass: 33976.488 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): High Five / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: P24941, EC: 2.7.1.37
#2: Chemical ChemComp-U73 / N-(5-ISOPROPYL-THIAZOL-2-YL)-2-PYRIDIN-3-YL-ACETAMIDE


Mass: 261.343 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H15N3OS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / Source method: isolated from a natural source / Formula: H2O / Water

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.12 Å3/Da / Density % sol: 41.48 %
Crystal growpH: 7.4
Details: 10 PERCENT PEG4000,50 MM AMMONIUM ACETATE, 50 MM HEPES PH 7.4

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 23, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→20 Å / Num. obs: 23407 / % possible obs: 97.4 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 12.2
Reflection shellResolution: 1.85→2 Å / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 4 / % possible all: 98.4

-
Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: OTHER / Resolution: 1.85→20 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.891 / SU B: 3.374 / SU ML: 0.106 / Cross valid method: THROUGHOUT / ESU R: 0.179 / ESU R Free: 0.167 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.272 1200 5.1 %RANDOM
Rwork0.223 ---
Obs0.226 22169 97.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 27.71 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2---1.53 Å20 Å2
3---1.52 Å2
Refinement stepCycle: LAST / Resolution: 1.85→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2215 0 18 67 2300
Refine LS restraints

Refinement-ID: X-RAY DIFFRACTION

TypeDev idealDev ideal targetNumber
r_bond_refined_d0.0160.0222289
r_bond_other_d0.0020.022142
r_angle_refined_deg1.5211.9763101
r_angle_other_deg0.91134985
r_dihedral_angle_1_deg6.3385272
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_chiral_restr0.1430.2350
r_gen_planes_refined0.0080.022465
r_gen_planes_other0.0040.02464
r_nbd_refined0.2210.2463
r_nbd_other0.2420.22454
r_nbtor_refined
r_nbtor_other0.0870.21342
r_xyhbond_nbd_refined0.1250.265
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined0.1310.212
r_symmetry_vdw_other0.2710.258
r_symmetry_hbond_refined0.1590.28
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it1.1041.51375
r_mcbond_other
r_mcangle_it1.94722231
r_mcangle_other
r_scbond_it2.5933914
r_scbond_other
r_scangle_it4.1094.5870
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
LS refinement shellResolution: 1.85→1.9 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.31 86
Rwork0.234 1606

+
About Yorodumi

-
News

-
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force. (see PDBe EMDB page)
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.: Q: What is "EMD"? / ID/Accession-code notation in Yorodumi/EM Navigator

External links: EMDB at PDBe / Contact to PDBj

-
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.

External links: wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

Read more

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more