[English] 日本語
Yorodumi
- PDB-4hco: Human Plk1-PBD in complex with Thymoquinone at the phophopeptide ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4hco
TitleHuman Plk1-PBD in complex with Thymoquinone at the phophopeptide binding site
ComponentsSerine/threonine-protein kinase PLK1
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / Kinase / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


Mitotic Telophase/Cytokinesis / regulation of protein localization to cell cortex / Mitotic Metaphase/Anaphase Transition / synaptonemal complex disassembly / Golgi inheritance / regulation of protein binding / Activation of NIMA Kinases NEK9, NEK6, NEK7 / homologous chromosome segregation / polo kinase / mitotic nuclear membrane disassembly ...Mitotic Telophase/Cytokinesis / regulation of protein localization to cell cortex / Mitotic Metaphase/Anaphase Transition / synaptonemal complex disassembly / Golgi inheritance / regulation of protein binding / Activation of NIMA Kinases NEK9, NEK6, NEK7 / homologous chromosome segregation / polo kinase / mitotic nuclear membrane disassembly / nuclear membrane disassembly / protein localization to nuclear envelope / Phosphorylation of Emi1 / metaphase/anaphase transition of mitotic cell cycle / synaptonemal complex / female meiosis chromosome segregation / Phosphorylation of the APC/C / anaphase-promoting complex binding / negative regulation of cyclin-dependent protein serine/threonine kinase activity / outer kinetochore / positive regulation of ubiquitin protein ligase activity / double-strand break repair via alternative nonhomologous end joining / microtubule bundle formation / mitotic chromosome condensation / Polo-like kinase mediated events / regulation of mitotic spindle assembly / Golgi Cisternae Pericentriolar Stack Reorganization / centrosome cycle / regulation of mitotic metaphase/anaphase transition / sister chromatid cohesion / positive regulation of ubiquitin-protein transferase activity / regulation of mitotic cell cycle phase transition / mitotic spindle assembly checkpoint signaling / mitotic spindle pole / mitotic G2 DNA damage checkpoint signaling / regulation of anaphase-promoting complex-dependent catabolic process / establishment of mitotic spindle orientation / mitotic sister chromatid segregation / positive regulation of proteolysis / mitotic cytokinesis / centriolar satellite / spindle midzone / negative regulation of double-strand break repair via homologous recombination / Regulation of MITF-M-dependent genes involved in cell cycle and proliferation / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Cyclin A/B1/B2 associated events during G2/M transition / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / protein localization to chromatin / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / positive regulation of peptidyl-threonine phosphorylation / Recruitment of NuMA to mitotic centrosomes / Resolution of Sister Chromatid Cohesion / Anchoring of the basal body to the plasma membrane / centriole / mitotic spindle organization / AURKA Activation by TPX2 / regulation of mitotic cell cycle / Condensation of Prophase Chromosomes / regulation of cytokinesis / RHO GTPases Activate Formins / establishment of protein localization / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / protein destabilization / kinetochore / spindle / spindle pole / positive regulation of protein localization to nucleus / Separation of Sister Chromatids / G2/M transition of mitotic cell cycle / microtubule cytoskeleton / The role of GTSE1 in G2/M progression after G2 checkpoint / Regulation of PLK1 Activity at G2/M Transition / double-strand break repair / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / mitotic cell cycle / peptidyl-serine phosphorylation / midbody / microtubule binding / regulation of cell cycle / protein kinase activity / protein ubiquitination / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / negative regulation of apoptotic process / protein kinase binding / chromatin / negative regulation of transcription by RNA polymerase II / magnesium ion binding / nucleoplasm / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
POLO box domain / 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. / Arylsulfatase, C-terminal domain / Serine/threonine-protein kinase, active site ...POLO box domain / 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. / Arylsulfatase, C-terminal domain / 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 / Alpha Beta
Similarity search - Domain/homology
Chem-IMW / Serine/threonine-protein kinase PLK1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsYin, Z. / Rehse, P.H.
CitationJournal: Acs Chem.Biol. / Year: 2013
Title: Thymoquinone Blocks pSer/pThr Recognition by Plk1 Polo-Box Domain As a Phosphate Mimic
Authors: Yin, Z. / Song, Y. / Rehse, P.H.
History
DepositionOct 1, 2012Deposition site: RCSB / Processing site: PDBJ
SupersessionOct 10, 2012ID: 4H70
Revision 1.0Oct 10, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2013Group: Database references
Revision 1.2Nov 8, 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_ref_seq_dif / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Serine/threonine-protein kinase PLK1
A: Serine/threonine-protein kinase PLK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,3454
Polymers55,0892
Non-polymers2562
Water1,856103
1
B: Serine/threonine-protein kinase PLK1


Theoretical massNumber of molelcules
Total (without water)27,5441
Polymers27,5441
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: Serine/threonine-protein kinase PLK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8013
Polymers27,5441
Non-polymers2562
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)33.260, 102.150, 67.740
Angle α, β, γ (deg.)90.00, 93.96, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Serine/threonine-protein kinase PLK1 / Polo-like kinase 1 / PLK-1 / Serine/threonine-protein kinase 13 / STPK13


Mass: 27544.373 Da / Num. of mol.: 2 / Fragment: UNP residues 367-603
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PLK1, PLK / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P53350, polo kinase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-IMW / 2-methyl-5-(1-methylethyl)cyclohexa-2,5-diene-1,4-dione / Thymoquinone / 2-isopropyl-5-methylbenzo-1,4-quinone


Mass: 164.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H12O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.08 Å3/Da / Density % sol: 40.98 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 1.4M Sodium Potassium Tartrate, 50mM MES pH 6.5, 100mM Hepes pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 29, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.75→51.07 Å / Num. obs: 11125 / % possible obs: 94.6 % / Redundancy: 2.4 % / Rmerge(I) obs: 0.154 / Net I/σ(I): 5.3
Reflection shellResolution: 2.75→2.9 Å / Redundancy: 2 % / Rmerge(I) obs: 0.387 / Mean I/σ(I) obs: 2.8 / Num. unique all: 1551 / % possible all: 91.5

-
Processing

Software
NameVersionClassification
MAR345dtbdata collection
MOLREPphasing
REFMAC5.5.0110refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UMW

1umw


Resolution: 2.75→51.07 Å / Cor.coef. Fo:Fc: 0.897 / Cor.coef. Fo:Fc free: 0.797 / SU B: 18.386 / SU ML: 0.375 / Cross valid method: THROUGHOUT / ESU R Free: 0.469 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2802 531 4.8 %RANDOM
Rwork0.20588 ---
obs0.20956 10576 94.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.541 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å20 Å20.04 Å2
2--0.04 Å20 Å2
3---0.07 Å2
Refinement stepCycle: LAST / Resolution: 2.75→51.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3519 0 18 103 3640
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0223609
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1261.9744881
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7425436
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.40222.988164
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.75815628
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3121529
X-RAY DIFFRACTIONr_chiral_restr0.0760.2543
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212699
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.3741.52187
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.71123515
X-RAY DIFFRACTIONr_scbond_it0.89631422
X-RAY DIFFRACTIONr_scangle_it1.5114.51366
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.75→2.821 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.435 33 -
Rwork0.286 754 -
obs--90.25 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
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.
  • 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 Accession Codes are Changing Soon! / 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.
  • 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

-
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.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

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