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- PDB-9fys: D11 mAbs bound to alpha-Bungarotoxin -

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Basic information

Entry
Database: PDB / ID: 9fys
TitleD11 mAbs bound to alpha-Bungarotoxin
Components
  • Alpha-bungarotoxin
  • D11 mAbs Light chain
  • heavy chain
KeywordsTOXIN / mAbs / bungarotoxin / antibody:toxin complex
Function / homology
Function and homology information


acetylcholine receptor inhibitor activity / ion channel regulator activity / toxin activity / extracellular region
Similarity search - Function
Snake toxin, conserved site / Snake toxins signature. / : / Snake toxin cobra-type / Snake three-finger toxin / Snake toxin-like superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Bungarus multicinctus (many-banded krait)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.32 Å
AuthorsWade, J. / Bohn, M.F. / Laustsen, A.H. / Morth, J.P.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)European Union
CitationJournal: To Be Published
Title: Structural mechanisms of a-neurotoxin-neutralizing antibodies enable rational design of pH-dependent antigen binding
Authors: Wade, J.
History
DepositionJul 3, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 16, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: heavy chain
X: Alpha-bungarotoxin
Z: Alpha-bungarotoxin
I: D11 mAbs Light chain
M: heavy chain
B: D11 mAbs Light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,3117
Polymers77,1166
Non-polymers1951
Water15,799877
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9100 Å2
ΔGint-37 kcal/mol
Surface area28740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.847, 83.804, 102.779
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

#1: Antibody heavy chain


Mass: 13187.223 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: heavy chain D11 / Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: Protein Alpha-bungarotoxin / Alpha-Bgtx / Alpha-Btx / Alpha-bungarotoxin / isoform A31 / Alpha-BTX A31 / Alpha-BgTx(A31) / Alpha- ...Alpha-Bgtx / Alpha-Btx / Alpha-bungarotoxin / isoform A31 / Alpha-BTX A31 / Alpha-BgTx(A31) / Alpha-bungarotoxin (A31) / BGTX A31 / Alpha-elapitoxin-Bm2a / Alpha-EPTX-Bm2a / Long neurotoxin 1


Mass: 10297.157 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bungarus multicinctus (many-banded krait)
Production host: Bungarus multicinctus (many-banded krait) / References: UniProt: P60615
#3: Antibody D11 mAbs Light chain


Mass: 15073.576 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 877 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.23 Å3/Da / Density % sol: 44.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M MES: NaOH, 12 % PEG 20000, pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.033 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 7, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.32→38 Å / Num. obs: 158875 / % possible obs: 97.2 % / Redundancy: 13.4 % / Biso Wilson estimate: 18.55 Å2 / CC1/2: 0.988 / CC star: 0.99 / Net I/σ(I): 8.99
Reflection shellResolution: 1.32→1.367 Å / Num. unique obs: 14966 / CC1/2: 0.47

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
DIALSv1.0data reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.32→25.17 Å / SU ML: 0.2319 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.0494
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1923 15121 5.06 %
Rwork0.1673 283583 -
obs0.1685 149352 95.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.22 Å2
Refinement stepCycle: LAST / Resolution: 1.32→25.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4942 0 12 877 5831
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01835177
X-RAY DIFFRACTIONf_angle_d1.5077045
X-RAY DIFFRACTIONf_chiral_restr0.1119756
X-RAY DIFFRACTIONf_plane_restr0.0171919
X-RAY DIFFRACTIONf_dihedral_angle_d7.5788755
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.32-1.330.42522350.43184289X-RAY DIFFRACTION43.15
1.33-1.350.40913110.42656350X-RAY DIFFRACTION63.97
1.35-1.370.42895130.40968522X-RAY DIFFRACTION85.89
1.37-1.380.41325090.3899355X-RAY DIFFRACTION94.34
1.38-1.40.38315810.37579464X-RAY DIFFRACTION96.51
1.4-1.420.34395360.35939685X-RAY DIFFRACTION97.32
1.42-1.440.37575460.34799683X-RAY DIFFRACTION97.54
1.44-1.460.34514720.32139713X-RAY DIFFRACTION97.57
1.46-1.490.31895330.3019626X-RAY DIFFRACTION97.91
1.49-1.510.30145770.27149676X-RAY DIFFRACTION98.03
1.51-1.540.26235340.25079755X-RAY DIFFRACTION98.07
1.54-1.560.26724960.24369840X-RAY DIFFRACTION98.3
1.56-1.590.26685090.23529728X-RAY DIFFRACTION98.4
1.59-1.630.23855480.22019757X-RAY DIFFRACTION98.44
1.63-1.660.24125550.219772X-RAY DIFFRACTION98.75
1.66-1.70.2195890.19029767X-RAY DIFFRACTION98.77
1.7-1.740.1984950.16969826X-RAY DIFFRACTION98.71
1.74-1.790.20124840.16449844X-RAY DIFFRACTION99.17
1.79-1.840.1864560.15699938X-RAY DIFFRACTION99.05
1.84-1.90.18874990.15879881X-RAY DIFFRACTION99.15
1.9-1.970.18594750.15729867X-RAY DIFFRACTION99.46
1.97-2.050.17655110.15279908X-RAY DIFFRACTION99.47
2.05-2.140.17995270.15119918X-RAY DIFFRACTION99.5
2.14-2.260.17985060.15269879X-RAY DIFFRACTION99.75
2.26-2.40.17225700.14069876X-RAY DIFFRACTION99.59
2.4-2.580.16595670.13949886X-RAY DIFFRACTION99.88
2.58-2.840.1614740.13839963X-RAY DIFFRACTION99.96
2.84-3.250.16724980.13999958X-RAY DIFFRACTION99.98
3.25-4.090.17164850.1389978X-RAY DIFFRACTION100
4.09-25.170.14695300.14059879X-RAY DIFFRACTION99.52
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)
13.83398708671-2.852283356092.944770936665.91822260502-2.423808520775.22242522123-0.0685981628626-0.2555847410430.3787927165690.159080501828-0.323561675906-0.565451322324-0.3688242495080.4445118586740.4418413744930.197349833272-0.0783227419751-0.01593944450930.3230316183910.01146845702680.25861577843611.2780107812-40.179737845127.7411518259
27.706497619190.443135678966-1.483819621823.6312490991.098707229262.72835935456-0.0977856474674-0.36744320072-0.3110228753950.217958503993-0.02346581363810.00606523064563-0.1164360791260.2336731923230.1272605437440.2214864802020.00323953132154-0.03278723533580.2739882999250.02897969552450.20366168325311.2060703124-58.239435479842.1836611465
31.62608931393-0.4254551724170.7253930321712.44457375183-0.4903475553982.39360729456-0.0227083009521-0.34265222894-0.06411436722710.1036648980590.05520309089540.0976035668536-0.0299447328719-0.109054490165-0.04267962203410.146564350552-0.004137067881430.004594221366160.3085808561760.02911917514330.1685774952371.00245204169-48.37111468232.2618741335
46.66378920872-1.69416352947-3.869653397716.136493542441.363381591712.28959453361-0.170415231203-0.053371700696-1.158831653130.04201678467930.04331489262760.229902650950.554973179264-0.5840958620320.08331277713590.233760923262-0.0361776707127-0.01969400167330.2574993845230.007856544841190.2885389197146.2327962367-62.982067612736.9250176641
51.078833245040.409509855329-0.667831534981.29995118781-0.5297758970142.09692344940.0840782685032-0.07551276222160.03335848294970.121297960403-0.0648708524621-0.0154430500657-0.19095094580.207434324031-0.01360802958250.168658178753-0.0105340236443-0.009840648239350.2402307093680.001844084063660.1609581055884.72933393818-42.816427620923.7747076908
66.06475652029-2.440915906231.611750061342.770756770581.288239408552.634893088130.0804592697030.568394993847-0.243410017212-0.278084427208-0.289550113978-0.4110716079180.3571929826760.1653284402060.3485869094340.1717084662440.00671655994063-0.0006235508581510.2710334424040.02186750676660.18442832146413.7379320703-58.192776396235.421935994
73.58538914773-2.75463335089-1.683031872863.72057851214-2.453642580089.52317656494-0.455626002467-0.694736933299-0.05523158392170.771938936008-0.0549522337923-0.439395062448-0.7202984614680.373461644840.4597583023570.358339752990.0065739159719-0.05715796120490.3183163337630.03759301354430.30097365628918.4930576558-63.665191978247.1288215113
82.2766693222-1.19454743612-0.9374982703262.31014542389-0.03690718184241.82777985370.02704193818110.192820507161-0.120520798628-0.188386729055-0.1066558841810.240405898703-0.0931595542376-0.3547495958140.03650827925640.1404500481460.00342783234354-0.01477665477580.156470734444-0.03605657266570.153770395014-21.2507241831-35.67636503638.88630663341
90.826988967247-0.452026101-0.01589772410541.79819705625-2.141475563238.719543044090.05213210983780.04763359338060.053171832131-0.199626599537-0.1233819205080.274299584723-0.45656376347-0.5715762676850.07324327084610.2697458058430.0571077128936-0.01310374034680.264663458864-0.04153668674360.239754883549-28.363538851-29.123572580214.850986317
104.30479118036-5.99578840394.077980428818.44802813277-5.798975289244.19963649646-0.01046065187390.6099260380550.187370492341-0.282846280694-0.191447127113-0.238551021321-0.5981553429810.3034635882940.3281644206980.302539835288-0.00336691833188-0.006318131602280.259320362-0.01041953323970.186166435877-16.3570264525-30.00915246273.88604947368
111.473873945390.7450049868590.1684777784942.06570757082-0.06462736661192.30207828315-0.08608786579850.0268380303635-0.1663682158990.132745253930.0508315480364-0.242209722091-0.04726380597760.3447449150030.04781095361290.1990555938510.02047214219650.006208205293820.2360865000870.04157564564730.186650219385-16.1217933569-35.597178305650.5173092672
125.101162213482.908926034774.580200352973.360555902613.271229927814.40490892384-0.2927415658530.373729008102-0.0500529688888-0.1776226775660.1626916661850.0216545799436-0.2708672772520.3185313420060.1194059723250.198189238064-0.0561219656790.01200020759930.2132477658190.009206546874370.153156997301-15.4421728984-31.169329675539.5935797214
130.8061670969740.1055187868010.9516363489250.5651054198560.03802378409613.80162069296-0.1329139153430.142411379641-0.114405155613-0.08217198523020.104320176555-0.0150255886227-0.1256993420880.1500639381880.06869501249530.168414874284-0.03475265164730.01414714065320.198817808121-0.007374574124630.163494064542-21.6366527016-35.715984932933.4455863257
140.2409932509040.2032840552221.414202607860.1394613813911.095297311267.729810003830.02336079068360.025542213334-0.291908823923-0.09897229826720.160672713532-0.192665895670.04756612904310.9033883699710.05198767389240.30290387718-0.08413788329170.005121099437570.4295343818020.008822206087130.255385503663-9.0839526216-30.091453837533.9849805028
153.515993319041.283124625140.7049562052132.904312155351.051486384921.70675495075-0.1405995334140.1281387964060.0157235638929-0.07985235999030.144093994632-0.0352206446204-0.3569160208860.0987265963873-0.02192125482020.21287714313-0.0323267286994-0.00637521054560.1870070127580.01952779547690.140682025037-17.7688242965-27.197161474845.0958517992
165.468490880251.065678464940.99139736296.519378683510.8416923479737.800411246070.3840729990650.01633986152730.235617353823-0.0115622504626-0.3049032060010.617771370277-0.443370572202-0.3478393045850.1036993446140.260018691570.01298093567960.0506912383570.2692602792570.03382567579730.285217835001-28.9855258938-28.797448176544.2869389907
176.585974738120.2481739680931.480325405813.51086308609-0.7382916998780.558179067379-0.02800360095410.00385867578927-0.3105689031520.10822643909-0.0585212920676-0.1215876041870.192490763722-0.08310343196380.179292887490.205040655864-0.0176626182831-0.0248992400620.1819560149090.02925421052240.12586179109-47.2443706781-57.377576025542.4571800301
181.91944814031.12013139484-0.7747899106992.65026819979-0.1449722938793.316613934250.0349650791276-0.175316103995-0.06769505528330.181961003611-0.0544280127949-0.18225918546-0.03522121161840.3186400530750.009583767439860.141205565435-0.0075835418791-0.008086349654180.215893989-0.01211016791990.145394488295-39.9192180522-48.562051597238.5322598406
195.23517901522-2.52971207909-0.1396116825775.76457137987-1.146129703433.690860534770.113628725717-0.08001566904220.1748853883120.491702044906-0.154777337498-0.330295806553-0.248892824850.1760614446940.04186755027560.240430433803-0.062413683542-0.01887293493910.232343969053-0.0301599075490.171517995893-43.0461499992-44.939591365244.0320765981
201.957571772541.35845222982-0.5060019346241.21243369552-0.1422041462560.4741057128450.0507313864448-0.0880829488025-0.05697425577670.0224338911847-0.0511972516008-0.0694549146239-0.03674200307150.0387995608795-0.002446199992170.161919901534-0.00756766020425-0.01394315615590.195360413890.003780425616550.156668033757-41.3617267-48.676682008637.3763365311
211.80147852711.203510006980.9628242287364.373086127343.323090146055.55729608845-0.0697338157092-0.1048352278130.2453384494450.0518908717181-0.1095940594690.435032039862-0.118852904887-0.5657433408280.04813938349030.1575133805720.0578901396314-0.007616092561220.24899356009-0.004866182334830.195298751095-49.9062548902-39.728368010122.4268768049
224.01697291176-0.31170743119-0.6858685633963.191127801341.003888135150.6891894235510.004592562875670.447312871377-0.407204659444-0.265185358649-0.06339462281520.0028265294649-0.267534434828-0.1684307893390.0467532006690.2304390435980.0115616408298-0.05683898801550.297590590025-0.07554600234630.267204167548-49.6394104317-55.87427086116.12602868002
232.024790635230.3535893088710.5273013273941.53593286680.7690477173532.028637123760.03990781014150.0789384648459-0.111550724943-0.0770310967764-0.018159469627-0.0283185749246-0.0706135839252-0.00251371201256-0.02468711847890.1364159296370.0105686702648-0.002265230773180.189615927447-0.01017533233450.153684329505-40.9960374601-46.994082719618.5625367169
242.606276024992.062965424312.692003922212.732894529931.811971087664.161049470540.113505592795-3.79078603631E-5-0.227394850284-0.201720627173-0.0209149116752-0.1774106926520.238504138035-0.145828117526-0.1624037281640.1830308769660.0001233687453440.003421461355540.207435032095-0.04953218064010.215863640473-55.4901625964-59.88722480325.99909435005
256.73886935433-0.01424938490120.2146897462062.090077862480.9087760883180.643899551091-0.06766743189320.0113397017123-0.380072350552-0.0169151349851-0.0231838730540.1495622772920.1280124000220.04929519777620.1349567002020.1530249113720.0235484248196-0.02784289146520.131429332882-0.01589568707870.1485055758438.46574105967-56.71619594086.32327845193
262.959464689410.207427105021-0.8907348210051.19861417771-0.1049798819860.630295567080.01593337227350.002773326881-0.39540398504-0.0702017038487-0.1119618287450.0664798547820.12532782225-0.04672888394090.09164200874180.190518542930.00951576754835-0.02466098998160.192390069602-0.01863960031230.192843406918-4.20005681829-53.83954060727.05855754676
271.33422446274-0.543816854159-0.3343283439321.15958936643-0.1102380405671.953856336060.000288165267249-0.04521808556360.002158717654260.0126310143172-0.0245389076717-0.04482127153210.01311876907870.1889895230990.01070153836650.146037293237-0.00531657932913-0.005112897485570.168857715166-0.002308181428940.1480463006454.37816848721-45.982732345113.0882847374
286.05735281881-0.344396688173-2.405298615813.356671174461.729611075836.138313803130.37409540359-0.1452978373910.460197898574-0.126363421308-0.231513440725-0.183917325944-0.6144009306080.135551534301-0.04511432693510.276755266449-0.02186586717880.02938823548910.218840750190.01556481883550.22833493272810.593753293-38.43334136859.85118258639
295.402910362981.89631176139-0.8205112888551.94058944568-0.4551097741961.15786295869-0.1072834159520.296032124423-0.187569732951-0.1801966957110.05633421251370.08846702703080.00536693291632-0.1698871044130.05148699553990.1889233794980.012848054602-0.01942718400560.196261042014-0.02188296012910.1979110514490.393615673373-49.92718027533.04119847064
302.92613822783-3.887179630012.828850104645.22781131302-3.848416156422.8934363924-0.202795460685-0.09041185391010.3342613220440.1745987859220.107197032213-0.31221964304-0.4122967494890.1943294308930.255064052290.183560140146-0.0113212797377-0.009336469422860.242711833957-0.001818894707460.19892128105218.1107302682-46.7142295366.26560117016
312.36137734989-0.84795965065-0.013741648660.588162589155-0.0753608314450.596281360360.0472073977165-0.204538749458-0.0678440493192-0.0114947423834-0.002103772935360.0595061739268-0.01817550220750.0047738009759-0.03892253990750.1681940933970.001908770891940.004366866650190.168786929856-0.007463014289020.17390205158-5.91752941163-45.417957323916.2123446754
329.55938317203-0.128258534925-2.688509362580.2118814257070.14261051942.45171076468-0.1048648005450.0939067496137-0.0100702366659-0.005694835749050.08641700354150.02394826699850.07888909931960.1018070922410.01117285136790.1631937941270.0385863953309-0.01057944784050.1465602360390.01172269793210.19110580217711.2696598006-54.718682845511.1212432877
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'C' and (resid 145 through 154 )CA145 - 1541 - 10
22chain 'C' and (resid 155 through 163 )CA155 - 16311 - 19
33chain 'C' and (resid 164 through 224 )CA164 - 22420 - 80
44chain 'C' and (resid 225 through 232 )CA225 - 23281 - 88
55chain 'C' and (resid 233 through 252 )CA233 - 25289 - 108
66chain 'C' and (resid 253 through 258 )CA253 - 258109 - 114
77chain 'C' and (resid 259 through 263 )CA259 - 263115 - 119
88chain 'X' and (resid 1 through 45 )XC1 - 451 - 45
99chain 'X' and (resid 46 through 60 )XC46 - 6046 - 60
1010chain 'X' and (resid 61 through 72 )XC61 - 7261 - 72
1111chain 'Z' and (resid 1 through 21 )ZD1 - 211 - 21
1212chain 'Z' and (resid 22 through 28 )ZD22 - 2822 - 28
1313chain 'Z' and (resid 29 through 45 )ZD29 - 4529 - 45
1414chain 'Z' and (resid 46 through 55 )ZD46 - 5546 - 55
1515chain 'Z' and (resid 56 through 68 )ZD56 - 6856 - 68
1616chain 'Z' and (resid 69 through 74 )ZD69 - 7469 - 74
1717chain 'I' and (resid 1 through 17 )IF1 - 171 - 17
1818chain 'I' and (resid 18 through 60 )IF18 - 6018 - 60
1919chain 'I' and (resid 61 through 76 )IF61 - 7661 - 76
2020chain 'I' and (resid 77 through 133 )IF77 - 13377 - 133
2121chain 'M' and (resid 145 through 154 )MG145 - 1541 - 10
2222chain 'M' and (resid 155 through 163 )MG155 - 16311 - 19
2323chain 'M' and (resid 164 through 252 )MG164 - 25220 - 108
2424chain 'M' and (resid 253 through 264 )MG253 - 264109 - 120
2525chain 'B' and (resid 1 through 17 )BH1 - 171 - 17
2626chain 'B' and (resid 18 through 32 )BH18 - 3218 - 32
2727chain 'B' and (resid 33 through 60 )BH33 - 6033 - 60
2828chain 'B' and (resid 61 through 67 )BH61 - 6761 - 67
2929chain 'B' and (resid 68 through 83 )BH68 - 8368 - 83
3030chain 'B' and (resid 84 through 91 )BH84 - 9184 - 91
3131chain 'B' and (resid 92 through 118 )BH92 - 11892 - 118
3232chain 'B' and (resid 119 through 133 )BH119 - 133119 - 133

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