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- PDB-6r4a: Aurora-A in complex with shape-diverse fragment 55 -

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Basic information

Entry
Database: PDB / ID: 6r4a
TitleAurora-A in complex with shape-diverse fragment 55
ComponentsAurora kinase A
KeywordsTRANSFERASE / Ser/Thr kinase Allosteric site
Function / homology
Function and homology information


Interaction between PHLDA1 and AURKA / regulation of centrosome cycle / axon hillock / cilium disassembly / spindle pole centrosome / mitotic centrosome separation / histone H3S10 kinase activity / chromosome passenger complex / regulation of G2/M transition of mitotic cell cycle / germinal vesicle ...Interaction between PHLDA1 and AURKA / regulation of centrosome cycle / axon hillock / cilium disassembly / spindle pole centrosome / mitotic centrosome separation / histone H3S10 kinase activity / chromosome passenger complex / regulation of G2/M transition of mitotic cell cycle / germinal vesicle / pronucleus / meiotic spindle organization / meiotic spindle / spindle organization / positive regulation of mitochondrial fission / mitotic spindle pole / spindle midzone / SUMOylation of DNA replication proteins / negative regulation of protein binding / liver regeneration / positive regulation of mitotic cell cycle / positive regulation of mitotic nuclear division / protein serine/threonine/tyrosine kinase activity / centriole / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / AURKA Activation by TPX2 / molecular function activator activity / regulation of signal transduction by p53 class mediator / mitotic spindle organization / regulation of cytokinesis / G2/M transition of mitotic cell cycle / response to wounding / regulation of protein stability / peptidyl-serine phosphorylation / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / kinetochore / spindle / microtubule cytoskeleton / mitotic cell cycle / Regulation of PLK1 Activity at G2/M Transition / protein autophosphorylation / spindle pole / ciliary basal body / midbody / microtubule / Regulation of TP53 Activity through Phosphorylation / basolateral plasma membrane / cell division / protein kinase activity / protein phosphorylation / non-specific serine/threonine protein kinase / postsynaptic density / protein heterodimerization activity / negative regulation of gene expression / protein serine kinase activity / ubiquitin protein ligase binding / protein serine/threonine kinase activity / centrosome / 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
ADENOSINE-5'-DIPHOSPHATE / Chem-JRT / Aurora kinase A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.937 Å
AuthorsBayliss, R. / McIntyre, P.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MR/K016903 United Kingdom
CitationJournal: Chemistry / Year: 2019
Title: Construction of a Shape-Diverse Fragment Set: Design, Synthesis and Screen against Aurora-A Kinase.
Authors: Zhang, R. / McIntyre, P.J. / Collins, P.M. / Foley, D.J. / Arter, C. / von Delft, F. / Bayliss, R. / Warriner, S. / Nelson, A.
History
DepositionMar 22, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 8, 2019Provider: repository / Type: Initial release
Revision 1.1May 22, 2019Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jul 10, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Jan 24, 2024Group: 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 / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aurora kinase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,04611
Polymers32,9651
Non-polymers1,08110
Water2,288127
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1920 Å2
ΔGint-56 kcal/mol
Surface area12760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.370, 81.370, 175.959
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-506-

CL

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Aurora kinase A / 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: 32964.637 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
Production host: Escherichia coli (E. coli)
References: UniProt: O14965, non-specific serine/threonine protein kinase

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Non-polymers , 6 types, 137 molecules

#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-JRT / 2-(benzimidazol-1-yl)-~{N}-(2-phenylethyl)ethanamide


Mass: 279.336 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H17N3O / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 127 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.55 Å3/Da / Density % sol: 51.78 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M Tris, pH 8.5: 0.5 M NaCl: 0.2 M MgCl2: 32.5 % v/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9282 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 6, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9282 Å / Relative weight: 1
ReflectionResolution: 1.937→29.33 Å / Num. obs: 26496 / % possible obs: 99.9 % / Redundancy: 18.9 % / CC1/2: 1 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.014 / Net I/σ(I): 32.1
Reflection shellResolution: 1.94→1.99 Å / Redundancy: 17 % / Rmerge(I) obs: 0.781 / Mean I/σ(I) obs: 3.7 / Num. unique obs: 1884 / CC1/2: 0.89 / Rpim(I) all: 0.193 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4CEG

4ceg


Resolution: 1.937→29.327 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.46
RfactorNum. reflection% reflection
Rfree0.2339 1334 5.05 %
Rwork0.1905 --
obs0.1928 26421 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.937→29.327 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2147 0 66 127 2340
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082264
X-RAY DIFFRACTIONf_angle_d1.1673072
X-RAY DIFFRACTIONf_dihedral_angle_d16.763871
X-RAY DIFFRACTIONf_chiral_restr0.059328
X-RAY DIFFRACTIONf_plane_restr0.005388
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9368-2.0060.2481350.20972405X-RAY DIFFRACTION99
2.006-2.08630.22011110.20392498X-RAY DIFFRACTION100
2.0863-2.18120.2461180.19512449X-RAY DIFFRACTION100
2.1812-2.29620.25911170.19262471X-RAY DIFFRACTION100
2.2962-2.440.23971440.1972461X-RAY DIFFRACTION100
2.44-2.62830.24631300.21072507X-RAY DIFFRACTION100
2.6283-2.89250.23651340.21242497X-RAY DIFFRACTION100
2.8925-3.31060.24421520.20272496X-RAY DIFFRACTION100
3.3106-4.16910.24831390.17782569X-RAY DIFFRACTION100
4.1691-29.32980.21111540.17742734X-RAY DIFFRACTION100
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.7771.02070.32822.12020.0970.7230.05360.0249-0.0828-0.18220.0646-0.18940.26970.093-0.09630.3111-0.0130.00410.3071-0.07560.311-0.549721.8757-12.12
22.64530.8596-0.47344.65470.26260.1702-0.14970.1991-0.0201-0.6745-0.08180.2702-0.4248-0.4739-0.01530.473-0.0103-0.04930.3666-0.09510.2364-16.254520.3333-17.0115
32.0565-1.1784-0.64182.64820.52510.650.05170.18250.0282-0.17560.08080.031-0.0059-0.0665-0.11560.2472-0.0212-0.01330.3262-0.00320.2059-14.727232.8853-11.0855
41.70060.33510.57191.95050.39372.60830.0920.0576-0.12310.03450.00370.16130.3378-0.3113-0.11180.2223-0.0184-0.00610.2902-0.00090.2959-27.979532.0117-3.7475
51.6684-0.0535-0.21662.5693-2.05311.6969-0.2318-0.4732-0.16610.449-0.02510.04930.0688-0.20.19970.36860.01780.07560.3069-0.02850.3193-28.338830.14957.7501
62.2368-0.1526-0.03682.89530.0012.1190.11040.25450.3885-0.174-0.06030.299-0.3025-0.22440.01320.22490.04690.00440.27850.02740.3537-30.0345.1233-4.3799
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 127 through 172 )
2X-RAY DIFFRACTION2chain 'A' and (resid 173 through 187 )
3X-RAY DIFFRACTION3chain 'A' and (resid 188 through 287 )
4X-RAY DIFFRACTION4chain 'A' and (resid 289 through 324 )
5X-RAY DIFFRACTION5chain 'A' and (resid 325 through 342 )
6X-RAY DIFFRACTION6chain 'A' and (resid 343 through 391 )

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