[English] 日本語
Yorodumi
- PDB-4jai: Crystal Structure of Aurora Kinase A in complex with N-{4-[(6-oxo... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4jai
TitleCrystal Structure of Aurora Kinase A in complex with N-{4-[(6-oxo-5,6-dihydrobenzo[c][1,8]naphthyridin-1-yl)amino]phenyl}benzamide
ComponentsAurora kinase A
Keywordstransferase/transferase inhibitor / KINASE INHIBITOR COMPLEX / ATP-BINDING / CELL CYCLE / CYTOPLASM / CYTOSKELETON / KINASE / NUCLEOTIDE-BINDING / PHOSPHOPROTEIN / SERINE/THREONINE-PROTEIN KINASE / TRANSFERASE / Protein kinase-like / transferase-transferase inhibitor complex
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 / positive regulation of oocyte maturation / pronucleus / 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 / positive regulation of oocyte maturation / pronucleus / mitotic centrosome separation / germinal vesicle / meiotic spindle / protein localization to centrosome / anterior/posterior axis specification / centrosome localization / neuron projection extension / spindle organization / positive regulation of mitochondrial fission / mitotic spindle pole / SUMOylation of DNA replication proteins / spindle midzone / regulation of G2/M transition of mitotic cell cycle / negative regulation of protein binding / centriole / protein serine/threonine/tyrosine kinase activity / 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 / AURKA Activation by TPX2 / liver regeneration / regulation of cytokinesis / regulation of signal transduction by p53 class mediator / 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 / regulation of protein stability / kinetochore / response to wounding / spindle / spindle pole / G2/M transition of mitotic cell cycle / mitotic spindle / Regulation of PLK1 Activity at G2/M Transition / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / mitotic cell cycle / peptidyl-serine phosphorylation / microtubule cytoskeleton / midbody / protein autophosphorylation / basolateral plasma membrane / Regulation of TP53 Activity through Phosphorylation / microtubule / proteasome-mediated ubiquitin-dependent protein catabolic process / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / protein kinase activity / postsynaptic density / ciliary basal body / protein phosphorylation / protein heterodimerization activity / cell division / negative regulation of gene expression / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / centrosome / ubiquitin protein ligase binding / negative regulation of apoptotic process / protein kinase binding / 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-XU2 / Aurora kinase A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsJiang, X. / Josephson, K. / Huck, B. / Goutopoulos, A. / Karra, S.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2013
Title: SAR and evaluation of novel 5H-benzo[c][1,8]naphthyridin-6-one analogs as Aurora kinase inhibitors.
Authors: Karra, S. / Xiao, Y. / Chen, X. / Liu-Bujalski, L. / Huck, B. / Sutton, A. / Goutopoulos, A. / Askew, B. / Josephson, K. / Jiang, X. / Shutes, A. / Shankar, V. / Noonan, T. / Garcia-Berrios, ...Authors: Karra, S. / Xiao, Y. / Chen, X. / Liu-Bujalski, L. / Huck, B. / Sutton, A. / Goutopoulos, A. / Askew, B. / Josephson, K. / Jiang, X. / Shutes, A. / Shankar, V. / Noonan, T. / Garcia-Berrios, G. / Dong, R. / Dhanabal, M. / Tian, H. / Wang, Z. / Clark, A. / Goodstal, S.
History
DepositionFeb 18, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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
A: Aurora kinase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4512
Polymers33,0451
Non-polymers4061
Water362
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)83.965, 83.965, 167.064
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

-
Components

#1: Protein Aurora kinase A / Aurora 2 / Aurora/IPL1-related kinase 1 / ARK-1 / Aurora-related kinase 1 / hARK1 / Breast tumor- ...Aurora 2 / Aurora/IPL1-related kinase 1 / ARK-1 / Aurora-related kinase 1 / hARK1 / Breast tumor-amplified kinase / Serine/threonine-protein kinase 15 / Serine/threonine-protein kinase 6 / Serine/threonine-protein kinase aurora-A


Mass: 33044.898 Da / Num. of mol.: 1 / Fragment: Aurora2 Kinase (UNP RESIDUES 122-396)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: AURKA, AIK, AIRK1, ARK1, AURA, AYK1, BTAK, IAK1, STK15, STK6
Production host: Escherichia coli (E. coli)
References: UniProt: O14965, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-XU2 / N-{4-[(6-oxo-5,6-dihydrobenzo[c][1,8]naphthyridin-1-yl)amino]phenyl}benzamide


Mass: 406.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H18N4O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 2.57 Å3/Da / Density % sol: 52.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 20% PEG MME 550, 0.1 M Bicine, 0.1 M NaCl , pH 9, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 14, 2008
RadiationMonochromator: Double Crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.11→30 Å / Num. all: 11697 / Num. obs: 11697 / % possible obs: 100 % / Observed criterion σ(I): 1.4 / Redundancy: 6.5 % / Rmerge(I) obs: 0.034
Reflection shellResolution: 3.11→3.23 Å / Rmerge(I) obs: 0.359 / % possible all: 100

-
Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.5.0066refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MQ4

1mq4


Resolution: 3.2→25 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.903 / SU B: 68.628 / SU ML: 0.552 / Cross valid method: THROUGHOUT / ESU R Free: 0.631 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.3182 468 7.6 %RANDOM
Rwork0.22408 ---
obs0.23096 5708 100 %-
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: 134.459 Å2
Baniso -1Baniso -2Baniso -3
1--1.15 Å2-0.57 Å20 Å2
2---1.15 Å20 Å2
3---1.72 Å2
Refinement stepCycle: LAST / Resolution: 3.2→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2054 0 31 2 2087
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0450.0222127
X-RAY DIFFRACTIONr_bond_other_d0.0060.021935
X-RAY DIFFRACTIONr_angle_refined_deg3.6951.9872876
X-RAY DIFFRACTIONr_angle_other_deg1.38434484
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.6555247
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.13122.745102
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.34315372
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6781519
X-RAY DIFFRACTIONr_chiral_restr0.1690.2305
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0212324
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02451
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_it5.3751.51243
X-RAY DIFFRACTIONr_mcbond_other0.3021.5500
X-RAY DIFFRACTIONr_mcangle_it17.24822004
X-RAY DIFFRACTIONr_scbond_it29.3713884
X-RAY DIFFRACTIONr_scangle_it40.7324.5872
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.205→3.287 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 29 -
Rwork0.322 399 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: -17.051 Å / Origin y: -33.021 Å / Origin z: 7.713 Å
111213212223313233
T0.0305 Å20.0319 Å2-0.0144 Å2-0.1198 Å20.0133 Å2--0.0276 Å2
L5.5712 °20.9985 °21.749 °2-2.1022 °21.9837 °2--2.0215 °2
S-0.2412 Å °-0.5044 Å °0.219 Å °-0.183 Å °0.0564 Å °0.1781 Å °-0.2078 Å °-0.0761 Å °0.1849 Å °

+
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