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- PDB-8vkb: Crystal structure of Plasmodium vivax glycylpeptide N-tetradecano... -

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Basic information

Entry
Database: PDB / ID: 8vkb
TitleCrystal structure of Plasmodium vivax glycylpeptide N-tetradecanoyltransferase (N-myristoyltransferase, NMT) bound to myristoyl-CoA and inhibitor 10b
ComponentsGlycylpeptide N-tetradecanoyltransferase
KeywordsTRANSFERASE / Enzyme / Inhibitor / Complex / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


glycylpeptide N-tetradecanoyltransferase / glycylpeptide N-tetradecanoyltransferase activity / metal ion binding / cytoplasm
Similarity search - Function
Glycylpeptide N-tetradecanoyltransferase, conserved site / Myristoyl-CoA:protein N-myristoyltransferase signature 1. / Myristoyl-CoA:protein N-myristoyltransferase signature 2. / Glycylpeptide N-tetradecanoyltransferase / Glycylpeptide N-tetradecanoyltransferase, N-terminal / Glycylpeptide N-tetradecanoyltransferase, C-terminal / Myristoyl-CoA:protein N-myristoyltransferase, N-terminal domain / Myristoyl-CoA:protein N-myristoyltransferase, C-terminal domain / Acyl-CoA N-acyltransferase
Similarity search - Domain/homology
: / TETRADECANOYL-COA / Glycylpeptide N-tetradecanoyltransferase
Similarity search - Component
Biological speciesPlasmodium vivax Sal-1 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.43 Å
AuthorsFenwick, M.K. / Staker, B.L. / Phan, I.Q. / Early, J. / Myler, P.J. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI155536 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93022C00036 United States
CitationJournal: J.Med.Chem. / Year: 2024
Title: Exploring Subsite Selectivity within Plasmodium vivax N -Myristoyltransferase Using Pyrazole-Derived Inhibitors.
Authors: Rodriguez-Hernandez, D. / Fenwick, M.K. / Zigweid, R. / Sankaran, B. / Myler, P.J. / Sunnerhagen, P. / Kaushansky, A. / Staker, B.L. / Grotli, M.
History
DepositionJan 8, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glycylpeptide N-tetradecanoyltransferase
B: Glycylpeptide N-tetradecanoyltransferase
C: Glycylpeptide N-tetradecanoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,29232
Polymers135,3023
Non-polymers5,99129
Water11,169620
1
A: Glycylpeptide N-tetradecanoyltransferase
hetero molecules


  • defined by author&software
  • 47.1 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)47,12710
Polymers45,1011
Non-polymers2,0269
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Glycylpeptide N-tetradecanoyltransferase
hetero molecules


  • defined by author&software
  • 47.2 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)47,17110
Polymers45,1011
Non-polymers2,0709
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Glycylpeptide N-tetradecanoyltransferase
hetero molecules


  • defined by author&software
  • 47 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)46,99512
Polymers45,1011
Non-polymers1,89411
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.366, 119.781, 176.883
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Glycylpeptide N-tetradecanoyltransferase


Mass: 45100.566 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium vivax Sal-1 (eukaryote) / Gene: PVX_085815 / Plasmid: pET11a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A5K1A2

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Non-polymers , 7 types, 649 molecules

#2: Chemical ChemComp-MYA / TETRADECANOYL-COA / MYRISTOYL-COA


Mass: 977.890 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C35H62N7O17P3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-A1AB8 / {1,5-dimethyl-4-[2-({(1P)-1-[2-(piperazin-1-yl)pyridin-4-yl]naphthalen-2-yl}oxy)ethyl]-1H-pyrazol-3-yl}(morpholin-4-yl)methanone


Mass: 540.656 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C31H36N6O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#7: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 620 / 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: 2.25 Å3/Da / Density % sol: 45.23 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop
Details: 0.2 M magnesium chloride, 0.1 M Tris, pH 8.5, and 20% PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1.00004 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 1, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00004 Å / Relative weight: 1
ReflectionResolution: 2.43→48.13 Å / Num. obs: 46174 / % possible obs: 99.1 % / Redundancy: 3.6 % / Biso Wilson estimate: 28.46 Å2 / CC1/2: 0.985 / Rmerge(I) obs: 0.159 / Rpim(I) all: 0.096 / Rrim(I) all: 0.186 / Χ2: 0.59 / Net I/σ(I): 5.3 / Num. measured all: 166469
Reflection shellResolution: 2.43→2.52 Å / % possible obs: 99.8 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.696 / Num. measured all: 16760 / Num. unique obs: 4540 / CC1/2: 0.559 / Rpim(I) all: 0.424 / Rrim(I) all: 0.82 / Χ2: 0.56 / Net I/σ(I) obs: 1.6

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Processing

Software
NameVersionClassification
XDSdata reduction
PHENIX1.20.1_4487refinement
Aimlessdata scaling
PHASERphasing
Cootmodel building
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.43→48.13 Å / SU ML: 0.2979 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.5578
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2326 2347 5.09 %
Rwork0.1849 43794 -
obs0.1873 46141 98.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.48 Å2
Refinement stepCycle: LAST / Resolution: 2.43→48.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9485 0 380 620 10485
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002210345
X-RAY DIFFRACTIONf_angle_d0.47114054
X-RAY DIFFRACTIONf_chiral_restr0.04151488
X-RAY DIFFRACTIONf_plane_restr0.00291741
X-RAY DIFFRACTIONf_dihedral_angle_d18.51343834
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.43-2.480.29561570.2382569X-RAY DIFFRACTION99.78
2.48-2.530.28061140.23552569X-RAY DIFFRACTION99.7
2.53-2.590.2861540.23312585X-RAY DIFFRACTION99.78
2.59-2.660.29861390.24382556X-RAY DIFFRACTION99.74
2.66-2.730.29951400.23542590X-RAY DIFFRACTION99.82
2.73-2.810.29151440.2232551X-RAY DIFFRACTION99.89
2.81-2.90.27141280.21912591X-RAY DIFFRACTION99.89
2.9-30.30491230.21222626X-RAY DIFFRACTION99.96
3-3.120.23611500.20162545X-RAY DIFFRACTION99.96
3.12-3.270.2471320.18762610X-RAY DIFFRACTION99.93
3.27-3.440.23441590.17612591X-RAY DIFFRACTION99.78
3.44-3.650.21311370.17342584X-RAY DIFFRACTION99.05
3.65-3.940.22511290.15872573X-RAY DIFFRACTION97.51
3.94-4.330.16261440.14752574X-RAY DIFFRACTION98.19
4.33-4.960.18591470.13262559X-RAY DIFFRACTION96.95
4.96-6.240.19261380.17162578X-RAY DIFFRACTION95.8
6.24-48.130.23821120.18472543X-RAY DIFFRACTION89.12
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)
12.52348901256-1.38819076423-2.059685117012.197081658133.15874649864.907937527720.169188597277-0.4427037028530.191850191329-0.00233922873870.1158468192190.0212783823907-0.219816397550.313331258548-0.2847298648210.170895555773-0.0522896345334-0.01635888349520.288287882917-0.04208894782420.32763115502543.381384434133.979602842826.0852722698
23.94778545249-0.192678459246-1.146951138611.98525269425-0.4187988158122.25454356950.1055728532660.0256312488119-0.072863133173-0.176491595368-0.03481781463610.03612307176850.3252374594660.129164499969-0.06096307063890.2619243090420.0197150639331-0.02641890401530.126901641116-0.03083998557950.21949413029232.888038651113.793966453811.2628956644
31.2946501628-1.1587375241-0.5475138121682.192653452492.247049937412.877429564380.08555314903980.1034872383410.0317790970491-0.2258140202330.0966406022697-0.294521544116-0.04007743386860.104769264741-0.155095476820.140104504963-0.0179959994670.02494792125020.1969481172920.02955294407850.19632292478734.982514661520.7472086658.51310043189
42.12962768481-2.274980832310.4501456140297.63580947911-0.4662798604630.1142782539020.0291338516895-0.08583117757350.1692133368650.272774686614-0.149160041398-0.148545452891-0.0389717071265-0.03721818512110.1087797735570.2457806206560.02670465030040.06815683949990.1888633962970.009193491897040.17027177959535.83059591822.300382136218.5525608473
53.444889912770.179676387373-2.40027669446.35634669696-3.450886297713.92165263030.1072569269490.09867712991260.0751747755659-0.172648340866-0.0830573716761-0.01523772341280.1295329255490.115650580719-0.01581061154280.195538999095-0.030249450228-0.05234744073060.152403092647-0.03915080061650.18709260400640.612670167427.630609863814.0543067828
60.5266047987310.548399016838-0.3848412566220.68786510083-0.2186837864770.601506429648-0.0729142547305-0.1335434015090.007315034097130.03369067961570.02535302190680.04204904655350.0481111373408-0.1172372407090.0400521756450.2722292884030.007429529315270.01141494831810.223325468107-0.002268639910540.3118306804449.8756151732916.616511828828.3742219301
72.54793576349-0.3751934516761.159802507531.264658494192.411843167546.02356943035-0.06375606574850.0981566796903-0.00227065030952-0.127324239948-0.01304240922390.0792816443568-0.343975054058-0.02511676287810.07255938293610.192709309781-0.0511255930360.02072874574640.1539638651840.05142721241010.24597465054216.712713864534.164403803512.3327495117
82.79492249801-1.0722718163-0.5353486433824.205942248591.056594415671.84059762726-0.05333053799060.188611168553-0.05221020644990.176147693436-0.01914466695530.2325850145470.0476039535072-0.0973410329390.05565641047990.162077555981-0.0269270585778-0.01559144539010.1737853465290.01828734699090.1245279505129.784704299723.069395102221.2405651887
98.19199048531.69773938825-2.357807693780.627466186899-0.7109598551261.60431469102-0.01636838849-0.298456667410.368611087946-0.00614939673118-0.04194311737310.129764352330.05421691457920.09749862869360.05810009915050.21616822629-0.023050176314-0.03322806151380.1327010019690.006224598217760.20266990540826.719241278629.277821546527.8528729475
102.51332551198-0.642877703498-2.000920888390.4729145753931.757909588846.58550150087-0.146091152077-0.01023759201820.0142163628168-0.015665355323-0.02786664892960.05189450899060.4661637957820.01220509842270.1616765820330.195609261418-0.0260647065983-0.04798121209760.235932490196-0.07387061054490.318460788832-3.5289939714942.044902920439.7878649544
114.21400898125-0.9636967038510.5954607908372.13805722062-1.237515987512.032173678180.112863650498-0.250743717471-0.07361376893370.04244990772930.0083587326926-0.09653446528690.1052296756220.0892808223158-0.09858756294850.199510198857-0.04484393732090.01018794561890.217377578279-0.03985848530090.2471743836086.2171748314646.630700214664.6352862621
121.45714458593-0.0148584910459-0.9481215309660.425479130644-1.025904705753.917519025640.0750510651703-0.2154835890110.1042212216320.176568739163-0.0127756286881-0.0944889429533-0.4213367566650.0135811546819-0.08181794655710.267367810580.00366158947825-0.02610075414910.198418359906-0.02409687095610.2678107740894.6930096566252.180324993959.5597512589
131.00902189273-0.0126788705493-0.07224221749311.74203426126-1.450705144322.13662141480.00721805650497-0.0171265226386-0.04613566368310.105268490221-0.0218583095981-0.1207761282890.0003202727372140.02429948937640.02093305976390.160520912372-0.0141130034525-0.0242490480440.168202711632-0.02746289089480.1771021246561.5551613942947.341674641352.1785807403
144.60303454216-2.590460449732.845501782742.39623944955-0.8269637628582.919592299530.176803666866-0.00913852085518-0.7363125359520.09117713981270.03115693818770.2003091444180.3298508433870.233738003267-0.205218186020.218305354092-0.007102373715570.05980668913340.2346984355720.0352049780730.36497717974622.867803400828.301997860354.3516627953
150.428895645020.01985959620050.6478624981538.6678192946-0.9877076568441.1043185928-0.05168989421160.0330669823624-0.27988561152-0.03266531901520.00367951186096-0.6244462669980.1204466496330.1833692474020.0532715873760.212793948578-0.0001385590099670.06626476889040.2738577052110.01700291234190.41752419924439.588762358937.710215538154.1448480954
162.26339155466-0.1576021674950.1015172900143.670669018750.3895931603256.413563178620.00376383976139-0.0781953717070.347776189457-0.245407297422-0.0567172432501-0.0590515477358-0.1597059365020.06111129810350.08871769813650.1229361353430.00320155768583-0.01357256042360.1274227616740.009672016325760.28498747845323.266632191954.968280724246.0303412834
172.473308391880.399737508194-0.7503248189193.19821506087-0.5974726381032.903608681570.0546182348362-0.134347413923-0.141792984396-0.027424249969-0.078133467015-0.077478307690.0592713037740.2192609984890.02839402770910.1101674997480.0123065555909-0.03294560748750.1884271129870.008134692108180.19660014435429.523831945741.282229929951.6701891528
182.91134483451-1.63228613031-1.945895813783.405819006110.2532518286561.58380984242-0.03628539118640.04055106978460.09519767882130.072769173285-0.0412326219936-0.1284718889080.0863413581838-0.08453750297210.09381871276190.23755373458-0.0362708763089-0.05941609347440.214857552923-0.07971852998180.24330391602910.123465696541.571096038441.9178394295
194.825715117782.49976581754-1.255662958624.01550146856-2.664913086941.81805270557-0.2536023034160.264599623908-0.305780905783-0.5287163491210.160190502403-0.3260332977220.554178144444-0.1880235458410.0802684875820.445366418169-0.006517743739790.008340651670710.260388557739-0.001439190424640.50506530920421.96307857259.172632269713.1093998236
203.194636660710.893954849483-0.2551346622392.07296401543-1.48176469472.20793437029-0.02892158311320.03435352500410.3520814286250.0386759547889-0.02545621901720.0235450803462-0.194803528983-0.007475133607180.05533760060120.2520753940420.005768785134460.02883357437720.165268861266-0.03812175740560.23545678420112.280007309482.39789307857.67558113009
211.263969758820.588632627580.8233355994731.02232547845-0.1875718884331.03668907150.001540334934250.0784034422105-0.148519477161-0.0912024622038-0.0596167982217-0.06693546536710.1245353429820.07084380320430.04768089661770.2196126407840.03580895824340.02366955281280.180797731925-0.04154371952120.25427421363313.379774737469.40123475058.58451402486
221.661553197512.816512578872.407597496215.222125349823.682730044735.73090262758-0.2888493961860.586808263166-0.258652396838-0.3545053943210.23516750629-0.4218660497990.1573558585730.8948644176430.06057233033610.2984005908150.0313113764971-0.01240986208430.4623832487080.1169332508340.426038727041-11.872478022968.1231802832-12.006007124
233.101560541580.1394451261410.3245534797071.96695506216-0.4984399023891.804190179280.00514985059623-0.00138325305845-0.0760425855498-0.09457310453590.03248746875660.08027897071350.0642060583825-0.165727223619-0.04086137347140.2017967139240.01222150527470.01669596251490.163677608823-0.005941717343480.198291224714-10.7116860169.396235685610.5507885349
245.158921026912.220487349381.409951946841.255511078681.331879732014.407933510330.2880459136030.0642088188474-0.441671468278-0.296895078218-0.119388403044-0.2115749746490.1679051612940.130060554854-0.1579842004560.2783097038630.04261134836940.03461077527760.122916682401-0.002983023813560.2896367602548.0414695177660.428351751311.1446323568
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 27 through 59 )AA27 - 591 - 33
22chain 'A' and (resid 60 through 116 )AA60 - 11634 - 90
33chain 'A' and (resid 117 through 150 )AA117 - 15091 - 124
44chain 'A' and (resid 151 through 174 )AA151 - 174125 - 148
55chain 'A' and (resid 175 through 198 )AA175 - 198149 - 172
66chain 'A' and (resid 199 through 257 )AA199 - 257173 - 231
77chain 'A' and (resid 258 through 296 )AA258 - 296232 - 270
88chain 'A' and (resid 297 through 379 )AA297 - 379271 - 353
99chain 'A' and (resid 380 through 410 )AA380 - 410354 - 384
1010chain 'B' and (resid 27 through 59 )BJ27 - 591 - 33
1111chain 'B' and (resid 60 through 116 )BJ60 - 11634 - 90
1212chain 'B' and (resid 117 through 150 )BJ117 - 15091 - 124
1313chain 'B' and (resid 151 through 198 )BJ151 - 198125 - 172
1414chain 'B' and (resid 199 through 234 )BJ199 - 234173 - 208
1515chain 'B' and (resid 235 through 257 )BJ235 - 257209 - 231
1616chain 'B' and (resid 258 through 296 )BJ258 - 296232 - 270
1717chain 'B' and (resid 297 through 386 )BJ297 - 386271 - 360
1818chain 'B' and (resid 387 through 410 )BJ387 - 410361 - 384
1919chain 'C' and (resid 26 through 59 )CW26 - 591 - 34
2020chain 'C' and (resid 60 through 150 )CW60 - 15035 - 125
2121chain 'C' and (resid 151 through 215 )CW151 - 215126 - 190
2222chain 'C' and (resid 216 through 241 )CW216 - 241191 - 216
2323chain 'C' and (resid 242 through 386 )CW242 - 386217 - 361
2424chain 'C' and (resid 387 through 410 )CW387 - 410362 - 385

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