[English] 日本語
Yorodumi
- PDB-2bmc: Aurora-2 T287D T288D complexed with PHA-680632 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2bmc
TitleAurora-2 T287D T288D complexed with PHA-680632
ComponentsSERINE THREONINE-PROTEIN KINASE 6
KeywordsTRANSFERASE / CELL CYCLE / SERINE/THREONINE-PROTEIN KINASE / ATP-BINDING / PHOSPHORYLATION
Function / homology
Function and homology information


Interaction between PHLDA1 and AURKA / regulation of centrosome cycle / axon hillock / spindle assembly involved in female meiosis I / cilium disassembly / spindle pole centrosome / chromosome passenger complex / histone H3S10 kinase activity / positive regulation of oocyte maturation / mitotic centrosome separation ...Interaction between PHLDA1 and AURKA / regulation of centrosome cycle / axon hillock / spindle assembly involved in female meiosis I / cilium disassembly / spindle pole centrosome / chromosome passenger complex / histone H3S10 kinase activity / positive regulation of oocyte maturation / mitotic centrosome separation / pronucleus / germinal vesicle / protein localization to centrosome / meiotic spindle / anterior/posterior axis specification / neuron projection extension / spindle organization / centrosome localization / positive regulation of mitochondrial fission / mitotic spindle pole / spindle midzone / SUMOylation of DNA replication proteins / negative regulation of protein binding / regulation of G2/M transition of mitotic cell cycle / liver regeneration / protein serine/threonine/tyrosine kinase activity / centriole / positive regulation of mitotic nuclear division / positive regulation of mitotic cell cycle / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / molecular function activator activity / regulation of signal transduction by p53 class mediator / AURKA Activation by TPX2 / regulation of cytokinesis / mitotic spindle organization / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / peptidyl-serine phosphorylation / regulation of protein stability / kinetochore / response to wounding / G2/M transition of mitotic cell cycle / spindle / spindle pole / mitotic spindle / Regulation of PLK1 Activity at G2/M Transition / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / mitotic cell cycle / protein autophosphorylation / microtubule cytoskeleton / midbody / basolateral plasma membrane / Regulation of TP53 Activity through Phosphorylation / proteasome-mediated ubiquitin-dependent protein catabolic process / microtubule / protein phosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / postsynaptic density / ciliary basal body / protein heterodimerization activity / negative regulation of gene expression / cell division / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / ubiquitin protein ligase binding / centrosome / protein kinase binding / negative regulation of apoptotic process / perinuclear region of cytoplasm / glutamatergic synapse / nucleoplasm / ATP binding / nucleus / cytosol
Similarity search - Function
Aurora kinase A / Aurora kinase / 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 ...Aurora kinase A / Aurora kinase / 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
Chem-MPY / Aurora kinase A
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsCameron, A.D. / Izzo, G. / Sagliano, A. / Rusconi, L. / Storici, P. / Fancelli, D. / Berta, D. / Bindi, S. / Catana, C. / Forte, B. ...Cameron, A.D. / Izzo, G. / Sagliano, A. / Rusconi, L. / Storici, P. / Fancelli, D. / Berta, D. / Bindi, S. / Catana, C. / Forte, B. / Giordano, P. / Mantegani, S. / Meroni, M. / Moll, J. / Pittala, V. / Severino, D. / Tonani, R. / Varasi, M. / Vulpetti, A. / Vianello, P.
CitationJournal: J.Med.Chem. / Year: 2005
Title: Potent and Selective Aurora Inhibitors Identified by the Expansion of a Novel Scaffold for Protein Kinase Inhibition.
Authors: Fancelli, D. / Berta, D. / Bindi, S. / Cameron, A. / Cappella, P. / Carpinelli, P. / Catana, C. / Forte, B. / Giordano, P. / Giorgini, M.L. / Mantegani, S. / Marsiglio, A. / Meroni, M. / ...Authors: Fancelli, D. / Berta, D. / Bindi, S. / Cameron, A. / Cappella, P. / Carpinelli, P. / Catana, C. / Forte, B. / Giordano, P. / Giorgini, M.L. / Mantegani, S. / Marsiglio, A. / Meroni, M. / Moll, J. / Pittala, V. / Roletto, F. / Severino, D. / Soncini, C. / Storici, P. / Tonani, R. / Varasi, M. / Vulpetti, A. / Vianello, P.
History
DepositionMar 11, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 17, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2019Group: Data collection / Source and taxonomy / Category: entity_src_gen / Item: _entity_src_gen.pdbx_host_org_cell_line
Revision 1.2Aug 21, 2019Group: Data collection / Derived calculations / Category: pdbx_struct_assembly / pdbx_struct_assembly_gen
Revision 1.3May 1, 2024Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: SERINE THREONINE-PROTEIN KINASE 6
B: SERINE THREONINE-PROTEIN KINASE 6
C: SERINE THREONINE-PROTEIN KINASE 6
D: SERINE THREONINE-PROTEIN KINASE 6
E: SERINE THREONINE-PROTEIN KINASE 6
F: SERINE THREONINE-PROTEIN KINASE 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)214,81712
Polymers211,8316
Non-polymers2,9866
Water3,603200
1
A: SERINE THREONINE-PROTEIN KINASE 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8032
Polymers35,3051
Non-polymers4981
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: SERINE THREONINE-PROTEIN KINASE 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8032
Polymers35,3051
Non-polymers4981
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: SERINE THREONINE-PROTEIN KINASE 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8032
Polymers35,3051
Non-polymers4981
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: SERINE THREONINE-PROTEIN KINASE 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8032
Polymers35,3051
Non-polymers4981
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: SERINE THREONINE-PROTEIN KINASE 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8032
Polymers35,3051
Non-polymers4981
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: SERINE THREONINE-PROTEIN KINASE 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8032
Polymers35,3051
Non-polymers4981
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)74.020, 101.219, 101.494
Angle α, β, γ (deg.)115.73, 92.40, 101.54
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.98263, -0.16561, 0.08374), (-0.14751, 0.42327, -0.89392), (0.1126, -0.89074, -0.44035)-36.9188, 0.46271, 7.15546
2given(0.98629, 0.16502, 0.00084), (0.07391, -0.43717, -0.89634), (-0.14755, 0.88411, -0.44337)3.11763, -18.89072, 48.66402
3given(-0.9882, -0.14777, -0.04033), (-0.11938, 0.57806, 0.80722), (-0.09597, 0.8025, -0.58888)-33.47494, -27.70596, 51.54625
4given(0.98319, 0.14029, -0.11683), (0.16774, -0.44148, 0.88145), (0.07208, -0.88624, -0.45759)-14.72044, 47.38321, 5.53947
5given(-0.99293, 0.00711, 0.11853), (-0.0069, -0.99997, 0.00213), (0.11854, 0.0013, 0.99295)-52.64313, 47.96092, 2.72248

-
Components

#1: Protein
SERINE THREONINE-PROTEIN KINASE 6 / AURORA-A / SERINE/THREONINE KINASE 15 / AURORA/IPL1-RELATED KINASE 1 / AURORA-RELATED KINASE 1 / ...AURORA-A / SERINE/THREONINE KINASE 15 / AURORA/IPL1-RELATED KINASE 1 / AURORA-RELATED KINASE 1 / HARK1 / BREAST-TUMOR-AMPLIFIED KINASE


Mass: 35305.164 Da / Num. of mol.: 6 / Fragment: CATALYTIC DOMAIN, RESIDUES 100-403 / Mutation: YES
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: O14965, EC: 2.7.1.37
#2: Chemical
ChemComp-MPY / (3E)-N-(2,6-DIETHYLPHENYL)-3-{[4-(4-METHYLPIPERAZIN-1-YL)BENZOYL]IMINO}PYRROLO[3,4-C]PYRAZOLE-5(3H)-CARBOXAMIDE


Mass: 497.591 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C28H31N7O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 200 / Source method: isolated from a natural source / Formula: H2O
Compound detailsFUNCTION: POSSIBLE ROLE IN CELL CYCLE REGULATION DURING ANAPHASE AND/OR TELOPHASE ENGINEERED ...FUNCTION: POSSIBLE ROLE IN CELL CYCLE REGULATION DURING ANAPHASE AND/OR TELOPHASE ENGINEERED RESIDUE IN CHAIN A, THR 287 TO ASP ENGINEERED RESIDUE IN CHAIN A, THR 288 TO ASP ENGINEERED RESIDUE IN CHAIN B, THR 287 TO ASP ENGINEERED RESIDUE IN CHAIN B, THR 288 TO ASP ENGINEERED RESIDUE IN CHAIN C, THR 287 TO ASP ENGINEERED RESIDUE IN CHAIN C, THR 288 TO ASP ENGINEERED RESIDUE IN CHAIN D, THR 287 TO ASP ENGINEERED RESIDUE IN CHAIN D, THR 288 TO ASP ENGINEERED RESIDUE IN CHAIN E, THR 287 TO ASP ENGINEERED RESIDUE IN CHAIN E, THR 288 TO ASP ENGINEERED RESIDUE IN CHAIN F, THR 287 TO ASP ENGINEERED RESIDUE IN CHAIN F, THR 288 TO ASP
Sequence detailsADDITIONAL 2 AMINO ACIDS AT N-TERMINUS DUE TO CLONING ARTIFACT. THE MUTATION IN THIS STRUCTURE THR ...ADDITIONAL 2 AMINO ACIDS AT N-TERMINUS DUE TO CLONING ARTIFACT. THE MUTATION IN THIS STRUCTURE THR 287 ASP AND THR 288 ASP ARE NOT PRESENT IN THE COORDINATES AND THEREFORE THERE ARE NO SEQADV RECORDS PRESENT.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.62 Å3/Da / Density % sol: 65.78 %
Crystal growpH: 4.6
Details: 2.5M NACL, 0.1M NAAC, 0.2M LISO4 WITH NON-DETERGENT SULFOBETAINE 195 AS ADDITIVE IN THE DROP, pH 4.60

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.93
DetectorType: ADSC CCD / Detector: CCD / Date: Jan 25, 2002
RadiationMonochromator: DIAMOND (111), GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 2.6→40 Å / Num. obs: 77069 / % possible obs: 97.4 % / Observed criterion σ(I): 2 / Redundancy: 2.4 % / Biso Wilson estimate: 47.1 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 6.9
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 2.1 / % possible all: 97.4

-
Processing

Software
NameVersionClassification
CNX2000refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: UNPUBLISHED STRUCTURE

Resolution: 2.6→29.95 Å / Rfactor Rfree error: 0.004 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: BULK SOLVENT MODEL USED. THE 6 MOLECULES OF THE ASYMMETRIC UNIT ARE ARRANGED IN 3 PAIRS OF DIMERS. WITHIN THESE DIMERS DOMAIN SWAPPING IS CLEARLY EVIDENT INVOLVING RESIDUES 292 TO 306 ...Details: BULK SOLVENT MODEL USED. THE 6 MOLECULES OF THE ASYMMETRIC UNIT ARE ARRANGED IN 3 PAIRS OF DIMERS. WITHIN THESE DIMERS DOMAIN SWAPPING IS CLEARLY EVIDENT INVOLVING RESIDUES 292 TO 306 ALTHOUGH FROM RESIDUES 304 TO 306 THE DENSITY IS RATHER POOR. RESIDUES 280-291 IN THE ACTIVATION LOOP BEFORE THIS REGION CANNOT BE OBSERVED
RfactorNum. reflection% reflectionSelection details
Rfree0.252 3885 5 %RANDOM
Rwork0.228 ---
obs-77042 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 36.5298 Å2 / ksol: 0.369773 e/Å3
Displacement parametersBiso mean: 48.7 Å2
Baniso -1Baniso -2Baniso -3
1-11.78 Å20.87 Å2-2.28 Å2
2---4.7 Å24.12 Å2
3----7.08 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.53 Å0.47 Å
Refinement stepCycle: LAST / Resolution: 2.6→29.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12672 0 222 200 13094
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.79
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.351.5
X-RAY DIFFRACTIONc_mcangle_it2.412
X-RAY DIFFRACTIONc_scbond_it1.912
X-RAY DIFFRACTIONc_scangle_it3.172.5
Refine LS restraints NCSNCS model details: RESTRAINTS / Rms dev Biso : 1.5 Å2 / Rms dev position: 0.5 Å / Weight Biso : 2 / Weight position: 10
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
Rfactor% reflection
Rfree0.385 5.3 %
Rwork0.353 -
obs-96.9 %
Xplor fileSerial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: 632.TOP

+
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