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- PDB-6s8k: Structure, Thermodynamics, and Kinetics of Plinabulin Binding to ... -

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Basic information

Entry
Database: PDB / ID: 6s8k
TitleStructure, Thermodynamics, and Kinetics of Plinabulin Binding to two Tubulin Isotypes
Components
  • Designed ankyrin repeat protein (DARPIN) D1
  • Tubulin alpha-1B chain
  • Tubulin beta-2B chain
KeywordsSTRUCTURAL PROTEIN / Tubulin / Microtubules / Microtubule targeting agents / Cancer
Function / homology
Function and homology information


positive regulation of axon guidance / microtubule-based process / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / structural constituent of cytoskeleton / microtubule cytoskeleton organization / microtubule cytoskeleton / nervous system development / mitotic cell cycle / microtubule / protein heterodimerization activity ...positive regulation of axon guidance / microtubule-based process / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / structural constituent of cytoskeleton / microtubule cytoskeleton organization / microtubule cytoskeleton / nervous system development / mitotic cell cycle / microtubule / protein heterodimerization activity / GTPase activity / GTP binding / metal ion binding / cytoplasm / cytosol
Similarity search - Function
Helix hairpin bin / Tubulin/FtsZ, C-terminal domain / Tubulin/FtsZ, GTPase domain / Ankyrin repeat-containing domain / 60s Ribosomal Protein L30; Chain: A; / Alpha tubulin / Tubulin-beta mRNA autoregulation signal. / Beta tubulin, autoregulation binding site / Beta tubulin / Tubulin ...Helix hairpin bin / Tubulin/FtsZ, C-terminal domain / Tubulin/FtsZ, GTPase domain / Ankyrin repeat-containing domain / 60s Ribosomal Protein L30; Chain: A; / Alpha tubulin / Tubulin-beta mRNA autoregulation signal. / Beta tubulin, autoregulation binding site / Beta tubulin / Tubulin / Tubulin, C-terminal / Tubulin C-terminal domain / Tubulin, conserved site / Tubulin subunits alpha, beta, and gamma signature. / Tubulin/FtsZ family, C-terminal domain / Tubulin/FtsZ-like, C-terminal domain / Tubulin/FtsZ, C-terminal / Tubulin/FtsZ, 2-layer sandwich domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ, GTPase domain / Tubulin/FtsZ, GTPase domain superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Helix Hairpins / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / Chem-PN6 / Tubulin alpha-1B chain / Tubulin beta-2B chain
Similarity search - Component
Biological speciessynthetic construct (others)
Bos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.52 Å
AuthorsSharma, A. / Olieric, N. / Steinmetz, M.
CitationJournal: Chem / Year: 2019
Title: Structure, Thermodynamics, and Kinetics of Plinabulin Binding to Two Tubulin Isotypes
Authors: La Sala, G. / Olieric, N. / Sharma, A.
History
DepositionJul 10, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 27, 2019Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
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.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tubulin alpha-1B chain
B: Tubulin beta-2B chain
F: Designed ankyrin repeat protein (DARPIN) D1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,4287
Polymers115,1013
Non-polymers1,3274
Water15,673870
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6370 Å2
ΔGint-40 kcal/mol
Surface area36770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.565, 91.351, 83.221
Angle α, β, γ (deg.)90.000, 96.851, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb

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Components

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Protein , 3 types, 3 molecules ABF

#1: Protein Tubulin alpha-1B chain / Alpha-tubulin ubiquitous / Tubulin K-alpha-1 / Tubulin alpha-ubiquitous chain


Mass: 48665.027 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P81947
#2: Protein Tubulin beta-2B chain


Mass: 49999.887 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q6B856
#3: Protein Designed ankyrin repeat protein (DARPIN) D1


Mass: 16435.645 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)

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Non-polymers , 5 types, 874 molecules

#4: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-PN6 / (3Z,6Z)-3-benzylidene-6-[(5-tert-butyl-1H-imidazol-4-yl)methylidene]piperazine-2,5-dione / Plinabulin


Mass: 336.388 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H20N4O2 / Feature type: SUBJECT OF INVESTIGATION / Comment: chemotherapy, anticancer, inhibitor*YM
#7: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 870 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.46 Å3/Da / Density % sol: 50.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 5.5
Details: 100 mM Bis-TrisMethane, pH 5.5, supplemented with 200 mM ammonium sulfate and 25% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 19, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.519→45.025 Å / Num. obs: 166365 / % possible obs: 99.02 % / Redundancy: 6.8 % / Biso Wilson estimate: 23.33 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.05515 / Rrim(I) all: 0.05971 / Net I/σ(I): 16.43
Reflection shellResolution: 1.519→1.574 Å / Rmerge(I) obs: 1.52 / Mean I/σ(I) obs: 1.21 / Num. unique obs: 15828 / CC1/2: 0.683 / Rpim(I) all: 0.629

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.52→45.02 Å / SU ML: 0.192 / Cross valid method: FREE R-VALUE / σ(F): 1.25 / Phase error: 24.024
RfactorNum. reflection% reflection
Rfree0.203 8315 5 %
Rwork0.1773 --
obs0.1786 166259 98.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 37.13 Å2
Refinement stepCycle: LAST / Resolution: 1.52→45.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7911 0 86 870 8867
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0048341
X-RAY DIFFRACTIONf_angle_d0.765811369
X-RAY DIFFRACTIONf_chiral_restr0.0481261
X-RAY DIFFRACTIONf_plane_restr0.00431484
X-RAY DIFFRACTIONf_dihedral_angle_d13.27424985
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.52-1.540.3864920.38059282X-RAY DIFFRACTION88.57
1.54-1.550.37275100.37059753X-RAY DIFFRACTION93.5
1.55-1.570.36465240.34639994X-RAY DIFFRACTION94.39
1.57-1.590.35755290.328610020X-RAY DIFFRACTION95.08
1.59-1.610.32775230.30559998X-RAY DIFFRACTION95.97
1.61-1.640.30185480.28910295X-RAY DIFFRACTION97.32
1.64-1.660.27855420.272910226X-RAY DIFFRACTION97.97
1.66-1.680.29195440.262310351X-RAY DIFFRACTION98.55
1.68-1.710.27435570.252110513X-RAY DIFFRACTION99.09
1.71-1.740.26525500.237410356X-RAY DIFFRACTION99.25
1.74-1.770.25565500.232110445X-RAY DIFFRACTION99.45
1.77-1.80.23365410.217310464X-RAY DIFFRACTION99.39
1.8-1.840.23125510.209910439X-RAY DIFFRACTION99.57
1.84-1.870.2165490.208210457X-RAY DIFFRACTION99.63
1.87-1.910.23925500.213410391X-RAY DIFFRACTION99.65
1.91-1.960.23645600.206210545X-RAY DIFFRACTION99.61
1.96-2.010.22225480.185410427X-RAY DIFFRACTION99.8
2.01-2.060.22225550.182810552X-RAY DIFFRACTION99.87
2.06-2.120.21415470.182410457X-RAY DIFFRACTION99.8
2.12-2.190.18815550.176210493X-RAY DIFFRACTION99.88
2.19-2.270.2185510.181310420X-RAY DIFFRACTION99.57
2.27-2.360.19745510.175910495X-RAY DIFFRACTION99.83
2.36-2.470.18865510.172810550X-RAY DIFFRACTION99.78
2.47-2.60.21025500.173910446X-RAY DIFFRACTION99.73
2.6-2.760.20365510.17410450X-RAY DIFFRACTION99.76
2.76-2.970.19695560.175810491X-RAY DIFFRACTION99.76
2.97-3.270.20485490.166110443X-RAY DIFFRACTION99.5
3.27-3.750.18795470.154410463X-RAY DIFFRACTION99.54
3.75-4.720.15895540.127610421X-RAY DIFFRACTION99.42
4.72-45.020.16075530.153210472X-RAY DIFFRACTION99.63
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)
14.744070251380.0260139911552-1.303151856691.615455301430.1864458607522.764866470170.0493081483108-0.143074182229-0.132867386858-0.0868597057496-0.0872270517378-0.02478751383720.08525432685650.4236685302410.07903555503450.173130825462-0.0229490747822-0.001208788903630.2253763580370.006387678647750.12991752731944.4260659317-0.46992354235510.7643327342
24.95565407109-0.486240799547-0.1542498894452.31178690688-0.1246891603031.22150720050.0728615706508-0.0377300796934-0.171670599057-0.262924975281-0.0688346233757-0.412752772460.3236506899251.08700404455-0.0007948676704560.26376821380.0634267014591-0.01253127131810.5959735957050.007497257302040.2472113337555.0162305336-2.9440930924311.7539831659
35.77881515765-1.032411967-0.6361040993731.017872676120.2331481626971.86391936031-0.0311857632854-0.359345178735-0.1756348996980.1103680449390.0120507713429-0.0204730756279-0.007475424669420.2952273485750.02562576823880.186366380184-0.04751551869060.007096291992130.2586947690210.01681241490040.14188897467741.76887294492.1314720449624.7049048589
44.146725529330.251467806109-0.3031724946320.94365162344-0.2865410411112.42931533502-0.0422306260948-0.1322814152690.03380598591780.03120658822850.0615629158969-0.0556409901123-0.2511625115420.165007961864-0.02177826982340.212954935034-0.0543451455440.03030128530320.125148743114-0.02776936687870.15962375622936.015379835411.384148261215.8242340946
52.511375856550.839049120598-0.3378884738981.81525171008-0.008101820971312.854192096510.06508683923070.04584372701220.03293748770880.0313588855755-0.04721130818740.0726403917966-0.07222376598280.112394707773-0.003617277247590.169486931586-0.006160701717520.00955761178360.141441167171-0.03041413876930.13071014635836.09056237544.684892503782.27431419892
62.261729038130.13213878294-1.564220121623.445120025210.5181583382954.30493195484-0.06496504076540.298965896042-0.181776018099-0.0389956711022-0.0309591085280.2138779653490.0992145720406-0.2758342596210.07996555871970.189716844404-0.0405768696581-0.05156304967880.234867608882-0.0143456437040.19366446001330.94053955140.142008026239-9.75234454089
71.84070081855-0.47146400544-1.432641665760.8625988600420.372316494412.12407802070.154306229440.2085825057310.0933417551823-0.191462044364-0.0619385998346-0.00559870063145-0.263917761049-0.0696289123096-0.07646190892050.251685295411-0.0254543456726-0.004861339005280.1779312233660.001435313678260.17370073292234.40414831368.83251166725-5.80867803761
82.035336325470.534176624872-2.046507482114.01151339853-4.072151018057.115685158750.105449569096-0.1117866139120.298995888206-0.01631924994610.02233469497480.0762105932454-0.422750503398-0.0711346240958-0.1597182059910.294420864781-0.002947084404710.06228936610540.177281891322-0.06309920900280.27336357568422.591998360319.69823740817.3782654708
92.82533313234-0.4540130177480.8104004463152.734933031760.9057390806963.773521836070.0322673346607-0.285521539565-0.8223649873410.07944825709790.119305600508-0.4718344086830.5494986437820.559510222051-0.05322845497660.2757961518660.0643972639696-0.05937910844790.395815508080.136027323810.57361559954720.8393025556-18.753065099441.9999802413
102.007949458990.458929361372-0.2234462937891.349977696670.1621883899261.72455183302-0.0179891054979-0.354637393646-0.236781321358-0.02091944164370.000878400542932-0.180509042669-0.01356537467360.250306300507-0.004675498933380.1538460115850.00629118017449-0.0146335508910.2989702827790.06622836552740.23036658722611.0259665018-6.4201467592342.2494454013
111.810502859070.376290730677-0.9079787579070.741876695665-0.1781456662382.05301787615-0.04335713000970.354527702669-0.2537497539-0.2270524772060.0281411504277-0.1219535647640.288446448641-0.1601198277480.03129088164380.245397104494-0.002806103619520.000775146361640.271485133514-0.006789004900860.2442713144045.0308173913-6.3327972219423.9107781666
124.047173224670.644637062045-2.824258746952.55578357536-0.9726129984055.811821528360.410765501574-0.361887971430.6319668043450.1790938368-0.127216632847-0.0730359126781-0.6347583865940.295944378938-0.2480502034740.219402256519-0.02528667524930.05636028212670.273635776942-0.02179865403130.392486815985-1.879843221568.0396554603344.296408017
136.25973449848-2.99146034682-3.655621242726.69139267042.349770337736.48276775258-0.0333870765385-0.644965029243-0.3700996240571.17014514993-0.0772523489792-0.06276425014190.467346291890.2823263869860.1576038495830.490299817027-0.0764927365939-0.07815973212550.6367176507150.1113293342380.2568921933-20.2709314973-2.284444874772.1651329336
142.924937958670.217506785787-1.348220917691.074842809120.08789815687493.953007386180.0329491956729-0.24599960488-0.1249657079040.168857357231-0.03613187182860.05529793803510.0513128098720.0320772922486-0.006225305357610.154948508359-0.01953470118840.01522629311140.2030327212410.01906726177270.171096690639-23.4903571494-1.1086825134255.11267106
157.33984464387-0.2681568996250.6400224996511.95771065675-0.2025552415648.72295722092-0.1236512052920.0514591093476-0.90375782606-0.1334564041450.0191680844032-0.09267883802810.793002501678-0.2459467443590.04783765218950.232488376628-0.05508081378360.02860405904460.185984356719-0.002050236658080.279876180096-24.1053939948-10.475147823742.5097369085
163.97738606408-1.22412944714-1.387921667694.60432603476-1.195836850743.68497448520.2471506196180.3666860112030.189041485711-0.278341306868-0.168282481185-0.258511251588-0.1765418850580.0426718837692-0.08435696272770.210260071408-0.00688835936601-0.02232433868540.283552605684-0.008502659474030.162646416283-21.26606829251.0518180040435.0118763787
178.1912384816-4.054404214181.084215886412.09299830327-0.3023979892397.08780037780.171216888640.926790783197-1.17765750371-0.643691693854-0.171742666340.6771490298120.459488501189-0.341241454728-0.05921589272620.288527490913-0.0311603009641-0.04034553811760.342726930613-0.08726901525440.375437572418-20.4353860112-10.214165507432.5131748572
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 28 )
2X-RAY DIFFRACTION2chain 'A' and (resid 29 through 72 )
3X-RAY DIFFRACTION3chain 'A' and (resid 73 through 127 )
4X-RAY DIFFRACTION4chain 'A' and (resid 128 through 197 )
5X-RAY DIFFRACTION5chain 'A' and (resid 198 through 273 )
6X-RAY DIFFRACTION6chain 'A' and (resid 274 through 311 )
7X-RAY DIFFRACTION7chain 'A' and (resid 312 through 401 )
8X-RAY DIFFRACTION8chain 'A' and (resid 402 through 437 )
9X-RAY DIFFRACTION9chain 'B' and (resid 1 through 88 )
10X-RAY DIFFRACTION10chain 'B' and (resid 89 through 259 )
11X-RAY DIFFRACTION11chain 'B' and (resid 260 through 401 )
12X-RAY DIFFRACTION12chain 'B' and (resid 402 through 440 )
13X-RAY DIFFRACTION13chain 'F' and (resid 13 through 36 )
14X-RAY DIFFRACTION14chain 'F' and (resid 37 through 125 )
15X-RAY DIFFRACTION15chain 'F' and (resid 126 through 134 )
16X-RAY DIFFRACTION16chain 'F' and (resid 135 through 158 )
17X-RAY DIFFRACTION17chain 'F' and (resid 159 through 167 )

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