[English] 日本語
Yorodumi
- PDB-7ayh: Crystal structure of Aurora A in complex with 7-(2-Anilinopyrimid... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7ayh
TitleCrystal structure of Aurora A in complex with 7-(2-Anilinopyrimidin-4-yl)-1-benzazepin-2-one derivative (compound 2c)
ComponentsAurora kinase AAurora A kinase
KeywordsTRANSFERASE / kinase / kinase inhibitor / aurora kinase / stk6 / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


Interaction between PHLDA1 and AURKA / regulation of centrosome cycle / germinal vesicle / axon hillock / spindle assembly involved in female meiosis I / spindle pole centrosome / positive regulation of oocyte maturation / chromosome passenger complex / pronucleus / histone serine kinase activity ...Interaction between PHLDA1 and AURKA / regulation of centrosome cycle / germinal vesicle / axon hillock / spindle assembly involved in female meiosis I / spindle pole centrosome / positive regulation of oocyte maturation / chromosome passenger complex / pronucleus / histone serine kinase activity / meiotic spindle / mitotic centrosome separation / protein localization to centrosome / anterior/posterior axis specification / neuron projection extension / centrosome localization / positive regulation of mitochondrial fission / spindle organization / mitotic spindle pole / SUMOylation of DNA replication proteins / spindle midzone / centriole / liver regeneration / regulation of G2/M transition of mitotic cell cycle / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / mitotic spindle organization / AURKA Activation by TPX2 / regulation of signal transduction by p53 class mediator / positive regulation of mitotic nuclear division / regulation of cytokinesis / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / cilium / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / mitotic spindle / microtubule cytoskeleton / negative regulation of protein binding / spindle / response to wounding / regulation of protein stability / G2/M transition of mitotic cell cycle / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Regulation of PLK1 Activity at G2/M Transition / midbody / mitotic cell cycle / microtubule / Regulation of TP53 Activity through Phosphorylation / non-specific serine/threonine protein kinase / peptidyl-serine phosphorylation / protein kinase activity / protein heterodimerization activity / protein autophosphorylation / cell division / centrosome / negative regulation of gene expression / protein serine kinase activity / protein serine/threonine/tyrosine kinase activity / protein serine/threonine kinase activity / ubiquitin protein ligase binding / protein phosphorylation / protein kinase binding / negative regulation of apoptotic process / perinuclear region of cytoplasm / nucleoplasm / ATP binding / nucleus / cytosol
Similarity search - Function
Aurora kinase A / Aurora kinase / Serine/Threonine protein kinases active-site signature. / Serine/threonine-protein kinase, active site / 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
Similarity search - Domain/homology
Chem-S9H / Aurora kinase A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsChaikuad, A. / Karatas, M. / Kunick, C. / Knapp, S. / Structural Genomics Consortium (SGC)
CitationJournal: Molecules / Year: 2021
Title: 7-(2-Anilinopyrimidin-4-yl)-1-benzazepin-2-ones Designed by a "Cut and Glue" Strategy Are Dual Aurora A/VEGF-R Kinase Inhibitors.
Authors: Karatas, M. / Chaikuad, A. / Berger, B. / Kubbutat, M.H.G. / Totzke, F. / Knapp, S. / Kunick, C.
History
DepositionNov 12, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 13, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 14, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Aurora kinase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3092
Polymers32,9491
Non-polymers3601
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area12880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.362, 83.362, 168.208
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

-
Components

#1: Protein Aurora kinase A / Aurora A kinase / Aurora 2 / Aurora/IPL1-related kinase 1 / hARK1 / Breast tumor-amplified kinase / Serine/threonine- ...Aurora 2 / Aurora/IPL1-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: 32948.781 Da / Num. of mol.: 1
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
Plasmid: pETM-11 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): -R3-pRARE2
References: UniProt: O14965, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-S9H / 7-[2-[(4-methoxyphenyl)amino]pyrimidin-4-yl]-1,3,4,5-tetrahydro-1-benzazepin-2-one


Mass: 360.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H20N4O2 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.56 Å3/Da / Density % sol: 51.96 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / Details: 24% PEG 3350, 0.2 M sodium malonate pH 7

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.99986 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Apr 19, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99986 Å / Relative weight: 1
ReflectionResolution: 2.8→44.28 Å / Num. obs: 9066 / % possible obs: 99.9 % / Redundancy: 8.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.038 / Rpim(I) all: 0.018 / Rrim(I) all: 0.051 / Net I/σ(I): 19.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.8-2.9590.9752.112790.8180.3551.077100
8.86-44.287.10.0313450.9980.0120.03498.4

-
Processing

Software
NameVersionClassification
Aimless0.7.1data scaling
REFMAC5.8.0222refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ONE
Resolution: 2.8→44.28 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.899 / SU B: 50.894 / SU ML: 0.446 / SU R Cruickshank DPI: 1.6239 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.624 / ESU R Free: 0.434 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.3126 466 5.1 %RANDOM
Rwork0.2726 ---
obs0.2746 8590 99.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 224.55 Å2 / Biso mean: 132.566 Å2 / Biso min: 79.57 Å2
Baniso -1Baniso -2Baniso -3
1--0.53 Å2-0.27 Å20 Å2
2---0.53 Å2-0 Å2
3---1.72 Å2
Refinement stepCycle: final / Resolution: 2.8→44.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2004 0 27 0 2031
Biso mean--111.96 --
Num. residues----250
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0142083
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171866
X-RAY DIFFRACTIONr_angle_refined_deg1.1411.6542825
X-RAY DIFFRACTIONr_angle_other_deg0.91.6414353
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0765248
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.80821.441111
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.97615346
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.4781515
X-RAY DIFFRACTIONr_chiral_restr0.0640.2261
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022442
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02402
LS refinement shellResolution: 2.8→2.873 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.431 34 -
Rwork0.379 605 -
all-639 -
obs--99.84 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
12.23872.51551.90383.66682.59651.8847-0.0514-0.40790.9708-0.3061-0.36860.259-0.283-0.43770.42010.48960.37070.22390.84810.20491.4386-4.0514-22.743812.6378
26.0065-0.20931.64563.2756-0.24343.3327-0.2079-0.82820.04650.2752-0.0060.2756-0.1164-0.35950.21380.04380.07860.07120.30520.17470.245-22.7-37.63814.927
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A125 - 205
2X-RAY DIFFRACTION2A206 - 390

+
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