[English] 日本語
Yorodumi
- PDB-2wtv: Aurora-A Inhibitor Structure -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2wtv
TitleAurora-A Inhibitor Structure
ComponentsSERINE/THREONINE-PROTEIN KINASE 6 AURORA/IPL1-RELATED KINASE 1, BREAST TUMOR-AMPLIFIED KINASE, AURORA-A, AURORA-RELATED KINASE 1, HARK1
KeywordsTRANSFERASE / KINASE / CELL CYCLE / PHOSPHOPROTEIN
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 / mitotic centrosome separation / pronucleus ...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 / mitotic centrosome separation / pronucleus / germinal vesicle / meiotic spindle / protein localization to centrosome / anterior/posterior axis specification / neuron projection extension / spindle organization / centrosome localization / positive regulation of mitochondrial fission / mitotic spindle pole / SUMOylation of DNA replication proteins / spindle midzone / negative regulation of protein binding / regulation of G2/M transition of mitotic cell cycle / 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 / regulation of cytokinesis / AURKA Activation by TPX2 / regulation of signal transduction by p53 class mediator / mitotic spindle organization / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H2AS121 kinase activity / histone H3S57 kinase activity / histone H3S28 kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / ribosomal protein S6 kinase activity / histone H2AT120 kinase activity / eukaryotic translation initiation factor 2alpha kinase activity / histone H2BS36 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H3S10 kinase activity / AMP-activated protein kinase activity / histone H3T11 kinase activity / histone H3T3 kinase activity / 3-phosphoinositide-dependent protein kinase activity / histone H3T45 kinase activity / liver regeneration / DNA-dependent protein kinase activity / histone H2AXS139 kinase activity / 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 / peptidyl-serine phosphorylation / Regulation of PLK1 Activity at G2/M Transition / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / mitotic cell cycle / microtubule cytoskeleton / protein autophosphorylation / midbody / basolateral plasma membrane / Regulation of TP53 Activity through Phosphorylation / proteasome-mediated ubiquitin-dependent protein catabolic process / microtubule / non-specific serine/threonine protein kinase / protein kinase activity / postsynaptic density / protein phosphorylation / ciliary basal body / protein heterodimerization activity / negative regulation of gene expression / cell division / 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
ACETATE ION / Chem-ZZL / Aurora kinase A
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsKosmopoulou, M. / Bayliss, R.
CitationJournal: Biochem.J. / Year: 2010
Title: Crystal Structure of an Aurora-A Mutant that Mimics Aurora-B Bound to Mln8054: Insights Into Selectivity and Drug Design.
Authors: Dodson, C.A. / Kosmopoulou, M. / Richards, M.W. / Atrash, B. / Bavetsias, V. / Blagg, J. / Bayliss, R.
History
DepositionSep 22, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 26, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: SERINE/THREONINE-PROTEIN KINASE 6 AURORA/IPL1-RELATED KINASE 1, BREAST TUMOR-AMPLIFIED KINASE, AURORA-A, AURORA-RELATED KINASE 1, HARK1
B: SERINE/THREONINE-PROTEIN KINASE 6 AURORA/IPL1-RELATED KINASE 1, BREAST TUMOR-AMPLIFIED KINASE, AURORA-A, AURORA-RELATED KINASE 1, HARK1
C: SERINE/THREONINE-PROTEIN KINASE 6 AURORA/IPL1-RELATED KINASE 1, BREAST TUMOR-AMPLIFIED KINASE, AURORA-A, AURORA-RELATED KINASE 1, HARK1
D: SERINE/THREONINE-PROTEIN KINASE 6 AURORA/IPL1-RELATED KINASE 1, BREAST TUMOR-AMPLIFIED KINASE, AURORA-A, AURORA-RELATED KINASE 1, HARK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,19330
Polymers132,9164
Non-polymers3,27826
Water13,385743
1
A: SERINE/THREONINE-PROTEIN KINASE 6 AURORA/IPL1-RELATED KINASE 1, BREAST TUMOR-AMPLIFIED KINASE, AURORA-A, AURORA-RELATED KINASE 1, HARK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9646
Polymers33,2291
Non-polymers7355
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: SERINE/THREONINE-PROTEIN KINASE 6 AURORA/IPL1-RELATED KINASE 1, BREAST TUMOR-AMPLIFIED KINASE, AURORA-A, AURORA-RELATED KINASE 1, HARK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,33312
Polymers33,2291
Non-polymers1,10511
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: SERINE/THREONINE-PROTEIN KINASE 6 AURORA/IPL1-RELATED KINASE 1, BREAST TUMOR-AMPLIFIED KINASE, AURORA-A, AURORA-RELATED KINASE 1, HARK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0107
Polymers33,2291
Non-polymers7816
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: SERINE/THREONINE-PROTEIN KINASE 6 AURORA/IPL1-RELATED KINASE 1, BREAST TUMOR-AMPLIFIED KINASE, AURORA-A, AURORA-RELATED KINASE 1, HARK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8865
Polymers33,2291
Non-polymers6574
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)118.707, 118.707, 135.890
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

-
Components

-
Protein , 1 types, 4 molecules ABCD

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


Mass: 33228.895 Da / Num. of mol.: 4 / Fragment: CATALYTIC DOMAIN, RESIDUES 122-403 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET M11 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): CODONPLUS RPIL
References: UniProt: O14965, non-specific serine/threonine protein kinase

-
Non-polymers , 5 types, 769 molecules

#2: Chemical
ChemComp-ZZL / 4-{[9-CHLORO-7-(2,6-DIFLUOROPHENYL)-5H-PYRIMIDO[5,4-D][2]BENZAZEPIN-2-YL]AMINO}BENZOIC ACID


Mass: 476.862 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C25H15ClF2N4O2
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 743 / Source method: isolated from a natural source / Formula: H2O

-
Details

Compound detailsENGINEERED RESIDUE IN CHAIN A, LEU 215 TO ARG ENGINEERED RESIDUE IN CHAIN A, THR 217 TO GLU ...ENGINEERED RESIDUE IN CHAIN A, LEU 215 TO ARG ENGINEERED RESIDUE IN CHAIN A, THR 217 TO GLU ENGINEERED RESIDUE IN CHAIN A, ARG 220 TO LYS ENGINEERED RESIDUE IN CHAIN B, LEU 215 TO ARG ENGINEERED RESIDUE IN CHAIN B, THR 217 TO GLU ENGINEERED RESIDUE IN CHAIN B, ARG 220 TO LYS ENGINEERED RESIDUE IN CHAIN C, LEU 215 TO ARG ENGINEERED RESIDUE IN CHAIN C, THR 217 TO GLU ENGINEERED RESIDUE IN CHAIN C, ARG 220 TO LYS ENGINEERED RESIDUE IN CHAIN D, LEU 215 TO ARG ENGINEERED RESIDUE IN CHAIN D, THR 217 TO GLU ENGINEERED RESIDUE IN CHAIN D, ARG 220 TO LYS
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.2 Å3/Da / Density % sol: 70.7 % / Description: NONE
Crystal growDetails: 0.8M NAH2PO4 1.2M K2HPO4 0.1M NA ACETATE, PH 4.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 2.4→59.3 Å / Num. obs: 83351 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Biso Wilson estimate: 24.36 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 12.3
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 3.2 / % possible all: 97.6

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OL7

1ol7


Resolution: 2.4→19.78 Å / SU ML: 0.3 / σ(F): 0.01 / Phase error: 21.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.211 3969 5 %
Rwork0.164 --
obs0.167 79206 94.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.14 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-5.6981 Å20 Å2-0 Å2
2--5.6981 Å20 Å2
3----11.3961 Å2
Refinement stepCycle: LAST / Resolution: 2.4→19.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8671 0 224 743 9638
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0069127
X-RAY DIFFRACTIONf_angle_d1.04612330
X-RAY DIFFRACTIONf_dihedral_angle_d21.4673396
X-RAY DIFFRACTIONf_chiral_restr0.0661288
X-RAY DIFFRACTIONf_plane_restr0.0041555
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4001-2.42930.29931440.22352379X-RAY DIFFRACTION83
2.4293-2.460.33651190.23262378X-RAY DIFFRACTION85
2.46-2.49230.3181220.2272423X-RAY DIFFRACTION85
2.4923-2.52640.32671170.22832547X-RAY DIFFRACTION88
2.5264-2.56240.30021190.22472521X-RAY DIFFRACTION88
2.5624-2.60050.28621460.2142485X-RAY DIFFRACTION89
2.6005-2.64110.28111380.19922599X-RAY DIFFRACTION90
2.6411-2.68430.22921360.19892596X-RAY DIFFRACTION92
2.6843-2.73040.28451280.19632625X-RAY DIFFRACTION92
2.7304-2.780.25281490.2012674X-RAY DIFFRACTION94
2.78-2.83330.25771320.18462708X-RAY DIFFRACTION95
2.8333-2.89090.22941420.18562709X-RAY DIFFRACTION95
2.8909-2.95360.23921380.18632661X-RAY DIFFRACTION95
2.9536-3.02210.23951520.18262742X-RAY DIFFRACTION97
3.0221-3.09740.21961510.16732732X-RAY DIFFRACTION97
3.0974-3.18080.18681600.15782751X-RAY DIFFRACTION97
3.1808-3.2740.22161400.15522769X-RAY DIFFRACTION98
3.274-3.37920.21151380.1522828X-RAY DIFFRACTION98
3.3792-3.49930.19231550.14122769X-RAY DIFFRACTION98
3.4993-3.63860.17941510.13542779X-RAY DIFFRACTION99
3.6386-3.80310.15231630.12752837X-RAY DIFFRACTION99
3.8031-4.0020.17441460.1252812X-RAY DIFFRACTION99
4.002-4.25040.14731420.11442833X-RAY DIFFRACTION99
4.2504-4.57490.15051420.11522819X-RAY DIFFRACTION99
4.5749-5.02840.1441280.11882837X-RAY DIFFRACTION100
5.0284-5.74040.20171620.15212783X-RAY DIFFRACTION99
5.7404-7.17450.20381590.16432811X-RAY DIFFRACTION100
7.1745-19.78510.151500.15262830X-RAY DIFFRACTION99

+
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