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- PDB-9c5k: Trypanosoma cruzi R19T/K20S/C64Y mutant beta-3-HBDH structure in ... -

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Basic information

Entry
Database: PDB / ID: 9c5k
TitleTrypanosoma cruzi R19T/K20S/C64Y mutant beta-3-HBDH structure in complex with NADPH and malonate
ComponentsHydroxybutyrate dehydrogenase
KeywordsOXIDOREDUCTASE / Trypanosoma cruzi / NADPH / malonate / beta-3-Hydroxybutyrate dehydrogenase
Function / homology
Function and homology information


3-hydroxybutyrate dehydrogenase activity / monocarboxylic acid metabolic process / 3-oxoacyl-[acyl-carrier-protein] reductase / lipid metabolic process
Similarity search - Function
3-hydroxybutyrate dehydrogenase / : / short chain dehydrogenase / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
ACETATE ION / MALONATE ION / Chem-NDP / 3-oxoacyl-[acyl-carrier-protein] reductase
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å
AuthorsHashimoto, H. / Debler, E.W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI165840 United States
CitationJournal: To Be Published
Title: Trypanosoma cruzi D-3-hydroxybutyrate dehydrogenase (HBDH) is NADP-dependent enzyme.
Authors: Hashimoto, H. / Debler, E.W.
History
DepositionJun 6, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 27, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hydroxybutyrate dehydrogenase
B: Hydroxybutyrate dehydrogenase
C: Hydroxybutyrate dehydrogenase
D: Hydroxybutyrate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,99528
Polymers114,3154
Non-polymers4,68024
Water15,205844
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20470 Å2
ΔGint-172 kcal/mol
Surface area33430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.350, 80.620, 124.340
Angle α, β, γ (deg.)90.000, 109.870, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Hydroxybutyrate dehydrogenase


Mass: 28578.861 Da / Num. of mol.: 4 / Mutation: R19T, K20S, C64Y
Source method: isolated from a genetically manipulated source
Details: genomic DNA / Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Strain: Sylvio X10/1 / Gene: C4B63_13g310 / Plasmid: pED714
Details (production host): His-3C-TcHBDH R19T/K20S/C64Y mutant
Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): RIL-codon plus / References: UniProt: A0A2V2VPF1

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Non-polymers , 6 types, 868 molecules

#2: Chemical
ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H30N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical
ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H2O4 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 844 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.44 Å3/Da / Density % sol: 49.59 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 25% PEG 3350, 0.1 M Li2SO4, 0.1 M BisTris pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033167 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 22, 2023
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033167 Å / Relative weight: 1
ReflectionResolution: 1.79→40.31 Å / Num. obs: 103427 / % possible obs: 99.9 % / Redundancy: 6.9 % / Biso Wilson estimate: 24.96 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.07 / Net I/σ(I): 15.7
Reflection shellResolution: 1.79→1.84 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.801 / Mean I/σ(I) obs: 3 / Num. unique obs: 7625 / CC1/2: 0.865 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.79→40.31 Å / SU ML: 0.1439 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 16.998
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.1678 2000 1.93 %Random
Rwork0.138 101411 --
obs0.1385 103411 99.91 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.93 Å2
Refinement stepCycle: LAST / Resolution: 1.79→40.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7769 0 293 846 8908
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01368234
X-RAY DIFFRACTIONf_angle_d1.32111211
X-RAY DIFFRACTIONf_chiral_restr0.07211308
X-RAY DIFFRACTIONf_plane_restr0.0121424
X-RAY DIFFRACTIONf_dihedral_angle_d14.06462913
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.79-1.830.23381420.20927183X-RAY DIFFRACTION99.88
1.83-1.880.23121410.19137199X-RAY DIFFRACTION99.88
1.88-1.940.21361420.17547185X-RAY DIFFRACTION99.93
1.94-20.19541420.15697225X-RAY DIFFRACTION99.93
2-2.070.15861430.14117203X-RAY DIFFRACTION99.99
2.07-2.160.18361430.13417235X-RAY DIFFRACTION99.97
2.16-2.260.13391430.13187242X-RAY DIFFRACTION99.93
2.26-2.370.17861420.1317225X-RAY DIFFRACTION99.96
2.37-2.520.16911430.13377232X-RAY DIFFRACTION99.89
2.52-2.720.16731420.1387232X-RAY DIFFRACTION99.89
2.72-2.990.16231440.14017289X-RAY DIFFRACTION99.93
2.99-3.420.15121420.14027245X-RAY DIFFRACTION99.92
3.42-4.310.1621450.12097304X-RAY DIFFRACTION99.95
4.31-40.310.16511460.13467412X-RAY DIFFRACTION99.72
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)
12.589952097930.6503857905951.176303969851.26974475977-0.270301144812.653296827430.1015605329850.1906597941630.358347182202-0.311473889436-0.135165445909-0.305487591405-0.09553284368660.1333343064620.02722635468580.28439149630.04508381018120.1120885297460.3008125087210.01514002581940.42123336187325.0116680767-9.0570771623113.8488301519
22.41178886386-1.6251128017-0.01576542561355.36534966081-2.200049983054.264559090060.3413715534130.528795489719-0.178304869072-1.03470538374-0.488818411779-0.3031207317020.4952127350420.369624363088-0.06598988881550.4313180990890.1273879590210.1240101259150.3937620524540.003158017090420.47127306499630.1667421248-17.5884813866.80807232674
32.05954833886-0.864983707372-0.07341581947564.17473034758-1.374267483583.526968661170.0589281382158-0.1601557585250.209888962331-0.0562745867901-0.0586149517592-0.7293753434150.07555943504080.5548063566750.04455517804450.2561710187990.05215034800760.05975477565250.37804347502-0.0281976861030.54507432163634.0348112717-16.681640750420.7108391353
40.9217616717930.40551476827-0.2322481148822.5198934223-0.007657061109651.1649693526-0.0435786520269-0.06451264924180.0587151315163-0.210520590659-0.00113391407666-0.3187927347360.1019700990610.137140353955-0.02878293985730.2642940908670.08685608400220.00860844523150.222441680915-0.02393558808810.28891860068218.5451553535-24.889330911821.0428265144
51.561798759020.5280561182880.1914047661653.747296693180.3950897446261.417312965050.03306206529140.0255316216388-0.05861696987440.03137914260820.0847184473133-0.6780715925150.1381948312610.335104371451-0.07245261523480.2466479964560.0587745979568-0.003349987479410.339270864752-0.03331576886590.33386740292423.6112839-20.87214962328.7184395115
60.7621544486010.2192821260990.027562513921.95721366541-0.08981402382691.076171797510.0488785400689-0.04411811338340.0848245164774-0.0360803646301-0.0323957748942-0.2064814645650.08883568856530.0321830534636-0.01591071565060.2206365306090.03929563659870.007073070250250.213068889031-0.02952010319020.23026255616713.1507033423-16.849607711124.8382609976
78.985516412037.515905483516.716318995457.805569813695.858119588655.031556496430.08713507476170.345776952826-0.412055011662-0.9614195774560.269452773215-0.6454043506790.5946816705730.461241952986-0.4121415177520.622108784470.07083521957370.03115522763140.281030408035-0.02516433088310.28706777042410.2489115036-32.39760108766.24262742145
80.5909090007170.4933040921240.942975192330.7116710501551.725087474484.387102201370.2501049141720.285681581981-0.0778248657541-1.15149257876-0.06198258741770.209167829951-0.116284525839-0.214993541103-0.09063272893720.7232576713320.0496475186496-0.03839271103410.281331863117-0.01987863368670.2155757877322.91737791133-28.82096430363.93808989928
91.34463651090.3495289295850.3092665785891.3515402548-0.007264084738761.593161711020.04532004795330.03727881390440.13992598264-0.1438393065610.02458130966-0.1719804831120.02531926104790.0680069790188-0.06714270455840.2654088630660.04220909833650.02721138662230.191727218423-0.02080906476280.2303763500238.8323912849-10.634712868116.8868798602
102.851344133540.8815437600060.3890025792884.11994805404-0.294774990424.72497348189-0.05946033281140.09856056499730.267614983643-0.297741916390.218335669997-0.157699692544-0.01910219772270.123178621527-0.2334132037310.3270288123640.008199303179730.04899669293420.142186689063-0.003595993298590.3064685787012.042325049479.0283196314211.6329085125
112.181561550191.08302305215-0.333876058513.26538797009-0.4788307655993.178709799370.112850547403-0.09642607432930.3529298132890.09703008771880.0697279484678-0.316569681592-0.2117968728430.138094507738-0.1677872505470.3295865603320.0007590171282690.06363685811490.182496232734-0.02100591655310.3797580664612.8157301316811.473391383615.9954357327
123.803674739630.652607968418-1.505438848053.119048987980.1610134581462.157296746670.1270978496760.00734113776530.553798908237-0.05383910185040.1562347155070.130505796315-0.453038656234-0.126203125876-0.272377313840.3881791907060.07558937606270.06695694103130.2177481706620.05557310216880.441186672688-7.1700201922715.902338263114.5471256355
130.7242532526830.122306248301-0.3610852935131.244566985-0.2096418427061.663931642280.0302967341682-0.01902812784520.1637317211110.02765385299470.1131296602550.0851478468182-0.155183910752-0.121364926056-0.1475820885530.240417658820.04170364310550.01005263420030.1870497841140.001456727443950.24310523175-7.99966416754-0.45684037906422.6297847243
145.533655526242.733991998470.3769118566894.724854714413.263503694432.85262974224-0.0639706772484-0.8818967326450.8787556143940.6589071193560.2558633850770.190332652103-0.863924028238-0.00748325037771-0.2244176731140.7786652020060.0949039518604-0.01612882017450.418158823388-0.1802517089110.44886183973-1.7876289058511.089752691542.4208539039
151.29011138747-0.921532593061-0.8859355177333.252543704421.992796071711.35081235476-0.33796225169-0.9531909952730.5171239580050.7383322380380.2841331216910.0264096612607-0.8499129132120.218471495341-0.3196672050540.8225109526350.0719710702159-0.1206056077070.520476818781-0.2825535852240.4316117713015.357032664857.3031901916545.2970968869
161.224416638730.2524321702180.3867065625951.80680294739-0.7854355063972.4097076950.00711711715322-0.06510263307120.1753210875230.05169654788730.0342777567187-0.17604864811-0.1611062334620.14934321016-0.03966121065890.2171968354180.02902243685760.01735796238620.178538206102-0.05384280220520.2536362849726.68799037924-2.1178671296523.8855920386
174.2115732736-0.2286134212580.6358995826372.644299020282.118541619453.58482416650.0375088475186-0.181316256175-0.3127838269030.1197763466760.0008662791910290.29541388470.298737498508-0.192250070635-0.06292468246870.255316796376-0.01905396932570.04895008610440.3270061829760.08412517259940.325756351455-26.733381529-24.500967353441.7185176371
183.05984780027-0.156138569604-0.01183383266445.58018750161-0.9115808220543.11971648160.1162348406-0.0225553163626-0.0642405857095-0.08624780326630.03980297641430.5979186773890.0278502668877-0.666228342068-0.1773917793290.1988490662270.03074442901190.04384714126220.4850073212380.09525677096070.40734197225-34.5942396367-17.01297373839.1719374104
190.791830518990.1450008019970.08143774110991.16495719264-0.4280678007472.10441630374-0.0039372274488-0.04214681220160.06410190629710.06169647167160.1442866281560.204044288795-0.0363361791424-0.231985394267-0.1372403581240.2086695006460.03443983212670.02051948375740.2522888905250.02921112036750.255233835825-17.9545681649-12.248888520732.9732346522
201.59052700016-2.90225676111-2.01125209415.565654287874.097132555063.213966404320.0273470960420.768357774175-0.000379521536922-0.6164282776570.0613724447191.006341644370.0642889931245-1.138488050870.01145179551920.545254412879-0.155176684847-0.2249992716850.6295059049120.1026987352830.442012611442-24.436510065-23.925644630513.1896223567
218.389235334592.252212967336.355177126770.8903580155272.051225506855.243039060760.5396137355530.523582073691-1.02960421078-0.389175864392-0.2169848050180.3241537902311.8138332062-0.361621724175-0.3728264446720.863234526591-0.146589389902-0.1849302871580.574998779815-0.03807048050370.400407331045-19.4498805751-30.665722916311.2367847381
221.53894635810.142008978725-0.3311921213071.831207296780.1699376895821.02388873084-0.002230924709590.0225565375864-0.062571781953-0.06087416111050.05694337206830.1770808478550.16169283895-0.184724899499-0.06918263226590.2596757625970.00765101582352-0.03624554328730.2112377372760.02543708468340.202757709526-12.0674971041-25.784276947732.8923999345
234.81921079786-1.241881903012.019533861053.538289522040.8326033991755.610373747950.0498272873044-0.186561098684-0.4118747252740.08814415738870.0845765522940.1823446923490.33758864962-0.369237147305-0.1521028061360.3710565746330.00322643414687-0.04083889908420.1791031890190.08545785682590.151044275894-4.33897292207-41.985992411745.5082105594
245.321151862790.1192130668141.551775957111.46246153204-0.2347712858393.598792905380.0579794926485-0.3276281811140.03614765799740.1590462952720.01155254151710.1774893817450.0577499912547-0.0809669007552-0.05699269186910.3583547702140.0396762169545-0.01735829476650.2239291523490.03063347722550.156837181614-1.106048522-38.778542875549.385409137
255.993487610311.7533835921-3.099533435922.14723382237-1.467807170074.395706606550.0562870316416-1.081204151930.05599213955130.563633580359-0.124871318068-0.239137025719-0.008618083429550.616651763961-0.1402266301060.5090058144340.0717625514144-0.1093126989490.3684809530890.006827719688550.2714577700786.62387177825-41.523995242556.0380225889
264.327597380271.47528027799-2.003427161871.70006117156-1.085576724152.97881478649-0.051422750651-0.00664720507599-0.240124119695-0.2082979847610.0631704456898-0.1564573757620.587476530550.2365316887410.0633368719670.4533427738560.105723562316-0.05832836773510.2567040031460.02038233481310.2388499847128.812795344-46.997647215142.9256790648
270.9429164361360.407657716660.08059808892251.45987627719-0.2102661414230.9072068261750.035898001748-0.01677958924390.0927496560910.112916856309-0.0164323588698-0.1207257228450.1420263282310.157263390903-0.0132860950130.2824891418260.064365183728-0.04494483115090.259772110873-0.02182823828780.21926626152212.2902250851-30.126512137341.2008138867
282.086658565711.145554495160.1204955482142.218876243090.1776438845351.301278835550.0745670304157-0.0798748006635-0.232410826880.0631612163488-0.0289202480538-0.3040689533120.3811923348140.167395224886-0.04818254683590.349585770430.0730636162086-0.04031453717920.218989894515-0.003367567074170.21382960445811.5373968905-36.650769455834.0744168553
290.6802025446470.141107228916-0.1179553738631.36986901458-0.2133215129340.8756634358720.00789415218162-0.07371847258570.01544812334610.006758067921110.03460180483240.0006259487786080.08945559596060.047129314035-0.03703253850610.2864071843060.0376685217572-0.03305786312980.210522751309-0.01503625392570.1790769940363.90000492617-27.506640161535.8275904304
306.931966463185.711893184934.593073077097.576580255223.987271147713.745311351090.252994482776-0.157861064978-0.3356027382280.5917404167290.0513864519181-0.5148539002580.2395903353420.364192179964-0.4296356528720.4355844601640.0182331014183-0.06863930240520.349652253049-0.06307858660050.23480705665215.0462790584-18.51825598455.1236410777
314.75659213571.81958149924.658226514342.344165553352.208624340955.31716697540.0468222350148-0.3408477336230.2945270975810.500981890698-0.2237089380310.114636417366-0.188006697953-0.3620855763160.2436632780450.402797863-0.0202853572032-0.02732012645370.289401315783-0.07394062888050.2291703949369.36000231859-11.826674766555.8933749827
321.254771410591.487306029740.4992799444154.577517165160.8900766777691.904880534020.0446768108267-0.1490994029220.024679698680.216382532660.02267170457660.1251789699540.0235974345327-0.0821643379158-0.06110859695480.2196488507640.0528067710386-0.01305495061570.21342576253-0.01269080658570.157254391491-4.54865596629-24.593303162642.2325884802
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 5 through 41 )AA5 - 411 - 37
22chain 'A' and (resid 42 through 58 )AA42 - 5838 - 54
33chain 'A' and (resid 59 through 85 )AA59 - 8555 - 81
44chain 'A' and (resid 86 through 108 )AA86 - 10882 - 104
55chain 'A' and (resid 109 through 137 )AA109 - 137105 - 133
66chain 'A' and (resid 138 through 195 )AA138 - 195134 - 191
77chain 'A' and (resid 196 through 209 )AA196 - 209192 - 205
88chain 'A' and (resid 210 through 225 )AA210 - 225206 - 221
99chain 'A' and (resid 226 through 266 )AA226 - 266222 - 262
1010chain 'B' and (resid 5 through 20 )BE5 - 201 - 16
1111chain 'B' and (resid 21 through 41 )BE21 - 4117 - 37
1212chain 'B' and (resid 42 through 85 )BE42 - 8538 - 81
1313chain 'B' and (resid 86 through 195 )BE86 - 19582 - 191
1414chain 'B' and (resid 196 through 209 )BE196 - 209192 - 205
1515chain 'B' and (resid 210 through 225 )BE210 - 225206 - 221
1616chain 'B' and (resid 226 through 266 )BE226 - 266222 - 262
1717chain 'C' and (resid 5 through 41 )CI5 - 411 - 37
1818chain 'C' and (resid 42 through 85 )CI42 - 8538 - 81
1919chain 'C' and (resid 86 through 195 )CI86 - 19582 - 191
2020chain 'C' and (resid 196 through 209 )CI196 - 209192 - 205
2121chain 'C' and (resid 210 through 223 )CI210 - 223206 - 219
2222chain 'C' and (resid 224 through 266 )CI224 - 266220 - 262
2323chain 'D' and (resid 4 through 20 )DN4 - 201 - 17
2424chain 'D' and (resid 21 through 41 )DN21 - 4118 - 38
2525chain 'D' and (resid 42 through 58 )DN42 - 5839 - 55
2626chain 'D' and (resid 59 through 85 )DN59 - 8556 - 82
2727chain 'D' and (resid 86 through 108 )DN86 - 10883 - 105
2828chain 'D' and (resid 109 through 137 )DN109 - 137106 - 134
2929chain 'D' and (resid 138 through 195 )DN138 - 195135 - 192
3030chain 'D' and (resid 196 through 209 )DN196 - 209193 - 206
3131chain 'D' and (resid 210 through 225 )DN210 - 225207 - 222
3232chain 'D' and (resid 226 through 266 )DN226 - 266223 - 263

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