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- PDB-9ms0: Structure of cord Blood MAIT A2 TCR in complex with human MR1-5-OP-RU -

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Basic information

Entry
Database: PDB / ID: 9ms0
TitleStructure of cord Blood MAIT A2 TCR in complex with human MR1-5-OP-RU
Components
  • A2-TRAV1-2-TRAJ12
  • A2-TRBV6-2-TRBJ1-2
  • Beta-2-microglobulin
  • Major histocompatibility complex class I-related gene protein
KeywordsIMMUNE SYSTEM / antigen presentation / MAIT cells / T cell receptor / MR1
Function / homology
Function and homology information


positive regulation of T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of exogenous antigen / MHC class I receptor activity / beta-2-microglobulin binding / antigen processing and presentation of peptide antigen via MHC class I / T cell receptor binding / negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions ...positive regulation of T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of exogenous antigen / MHC class I receptor activity / beta-2-microglobulin binding / antigen processing and presentation of peptide antigen via MHC class I / T cell receptor binding / negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide antigen assembly with MHC class II protein complex / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / MHC class II protein complex / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / regulation of erythrocyte differentiation / HFE-transferrin receptor complex / response to molecule of bacterial origin / MHC class I peptide loading complex / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / MHC class I protein complex / peptide antigen binding / positive regulation of T cell activation / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / specific granule lumen / phagocytic vesicle membrane / recycling endosome membrane / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / MHC class II protein complex binding / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / positive regulation of cellular senescence / tertiary granule lumen / DAP12 signaling / T cell differentiation in thymus / negative regulation of neuron projection development / ER-Phagosome pathway / protein refolding / early endosome membrane / protein homotetramerization / defense response to Gram-negative bacterium / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / defense response to Gram-positive bacterium / immune response / endoplasmic reticulum lumen / Amyloid fiber formation / Golgi membrane / innate immune response / lysosomal membrane / external side of plasma membrane / focal adhesion / Neutrophil degranulation / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane / cytosol
Similarity search - Function
MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / : / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. ...MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / : / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Chem-Q87 / Beta-2-microglobulin / Major histocompatibility complex class I-related protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.52 Å
AuthorsAwad, W. / Rossjohn, J.
Funding support Australia, 2items
OrganizationGrant numberCountry
Australian Research Council (ARC)DE220101491 Australia
National Health and Medical Research Council (NHMRC, Australia) Australia
CitationJournal: To Be Published
Title: Structure of human MAIT BV28 TCR in complex with human MR1-5-OP-RU
Authors: Awad, W. / Rossjohn, J.
History
DepositionJan 9, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 14, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Major histocompatibility complex class I-related gene protein
B: Beta-2-microglobulin
C: A2-TRAV1-2-TRAJ12
D: A2-TRBV6-2-TRBJ1-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,6695
Polymers93,3384
Non-polymers3301
Water6,323351
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.526, 114.533, 141.393
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab

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Components

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Protein , 3 types, 3 molecules ABD

#1: Protein Major histocompatibility complex class I-related gene protein / MHC class I-related gene protein / Class I histocompatibility antigen-like protein


Mass: 31711.670 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MR1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q95460
#2: Protein Beta-2-microglobulin


Mass: 11748.161 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Production host: Escherichia coli (E. coli) / References: UniProt: P61769
#4: Protein A2-TRBV6-2-TRBJ1-2


Mass: 27234.393 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)

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Antibody , 1 types, 1 molecules C

#3: Antibody A2-TRAV1-2-TRAJ12


Mass: 22644.096 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)

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Non-polymers , 2 types, 352 molecules

#5: Chemical ChemComp-Q87 / 1-deoxy-1-({2,6-dioxo-5-[(E)-(2-oxopropylidene)amino]-1,2,3,6-tetrahydropyrimidin-4-yl}amino)-D-ribitol


Mass: 330.294 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H18N4O7 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 351 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.75 Å3/Da / Density % sol: 55.26 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: PEG3350, Na-acetate, BTP / PH range: 6.3

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 1, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.52→46.84 Å / Num. obs: 34953 / % possible obs: 99.57 % / Redundancy: 2 % / CC1/2: 0.997 / CC star: 0.999 / Net I/σ(I): 10.2
Reflection shellResolution: 2.52→2.59 Å / Num. unique obs: 2871 / CC1/2: 0.768

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.52→46.84 Å / SU ML: 0.3006 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.4175
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2131 1728 4.94 %
Rwork0.1797 33219 -
obs0.1822 34953 99.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.92 Å2
Refinement stepCycle: LAST / Resolution: 2.52→46.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6270 0 22 353 6645
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00226510
X-RAY DIFFRACTIONf_angle_d0.55068862
X-RAY DIFFRACTIONf_chiral_restr0.0419950
X-RAY DIFFRACTIONf_plane_restr0.00381153
X-RAY DIFFRACTIONf_dihedral_angle_d14.02142328
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.52-2.590.31951370.27312734X-RAY DIFFRACTION99.65
2.59-2.680.30341420.26672718X-RAY DIFFRACTION99.44
2.68-2.770.28851540.24162724X-RAY DIFFRACTION99.65
2.77-2.880.28911270.24372739X-RAY DIFFRACTION99.72
2.88-3.020.28281440.2372747X-RAY DIFFRACTION99.66
3.02-3.170.281340.21162747X-RAY DIFFRACTION99.76
3.17-3.370.21651370.19362753X-RAY DIFFRACTION99.38
3.37-3.630.21321690.17832732X-RAY DIFFRACTION99.69
3.63-40.18841410.15422767X-RAY DIFFRACTION99.73
4-4.580.17191630.13112792X-RAY DIFFRACTION99.83
4.58-5.760.15761440.13492814X-RAY DIFFRACTION99.56
5.77-46.840.1911360.17642952X-RAY DIFFRACTION98.82
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)
10.3987122435860.1746737834670.4627639738010.826555016314-0.1269994784010.3438533448110.07726150711450.04890837258680.06903224684440.12331981666-0.08276068306540.0510088663474-0.286229776288-0.1084831690869.15154334024E-60.3564170942860.003335538979830.02062255623470.2114322840160.01984998349260.22195521995524.28929247219.4472864414-15.9988571707
20.3143240090050.427851195291-0.2867107098721.19826580879-0.001836261722270.5773222572070.1558133939730.0318123692044-0.07428429925350.24496324586-0.158655775968-0.117073894826-0.07847188407730.0319672738183-0.005141065221510.323618570127-0.034706952235-0.006246524369810.2589334867620.03384391399650.22639768601928.042349833710.6383318132-9.40031107401
30.2603909997470.155679066875-0.3811535582780.729671428764-0.0310872667550.2576053110570.0135984636350.0331767966225-0.1137850030570.07654115867840.0311279222204-0.0234496260435-0.09246376710830.07957833016093.82749939092E-60.2659058689060.00549604057347-0.03619408841030.2706732835830.01758638427820.28097648829633.71829717567.1346307264-17.1951645541
40.593780093406-0.1701695766430.4088648179550.2869373240240.1168482209750.4984052927670.0388628727428-0.092557740846-0.07960412331140.187286351925-0.0681200052959-0.09378525795090.005045435999930.1191197404353.58924360396E-60.345284924356-0.0410925800369-0.03474994806560.3308673755340.03686552847480.27240342011949.963140296635.0462451579-27.7141998889
51.999884989252.000033217432.000164957622.000065519791.999799346141.99998388563-0.8623429676497.16251333393-6.5200672978-2.380115098752.29869828493-1.152763861413.376307398521.10442661659-1.455365240171.53345463585-0.477708382520.3423915352510.7399434378610.06192425574450.97946139533960.035585693345.1856247448-35.3026217516
60.03571467408640.005719223774350.02935263392240.02140112544850.02204920814250.0301633374611-0.270618473115-0.154587581996-0.1870111214180.293107986349-0.020748397084-0.332724272768-0.04928987892770.165320130313-1.24092895077E-50.656027209398-0.0611286266472-0.05166252923820.4799091111660.007802248856690.33296277491940.781807461525.074107199-0.662827619733
70.0157030942969-0.0215342060654-0.003727893274450.0135383063461-0.002494421551510.01684887566230.267585497715-0.046439197022-0.294557601783-0.09052348651560.095919844185-0.16289517905-0.0293315121559-0.119409489947-0.0003544361710420.473594070875-0.015522759583-0.08728761135260.3731459984430.04365716038970.369296198239.744256123238.1983314972-13.6558331847
80.1578410632440.0461782821327-0.1695220446470.00652519787539-0.04114310150.1734375759890.2117931305570.7476669757290.988352547988-0.174584273808-0.1999928292950.0252213635923-0.0879202887060.188892641241-0.01278210679110.717309785711-0.05567648321040.007992887801290.405162683650.1405566159820.47922172903435.892441580848.4440733207-24.2202503987
90.06843302050330.0442706052664-0.01193545124030.06356670979520.0816215952280.08007976710150.183368140076-0.0811126381179-0.01244409370130.232502817126-0.225194306265-0.186155562646-0.1980908322350.0230769515999-9.46673649138E-50.443309517014-0.01956737209020.00830388296320.368030834316-0.01183293663890.2769380297234.569138583337.8567143607-14.7822180393
100.01658108065930.04153503092680.08365107929890.03882939939290.05431680338020.05242192297680.0083965153727-0.08941660699590.01440006549920.597939165644-0.03313177778480.48254027487-0.0587647340546-0.284369957352-6.16216824481E-50.54215271754-0.02301244054590.02527840912640.35314016733-0.0394316776480.30026144440631.637598265935.8766254685-4.43816138269
110.0161478341481-0.00296891050839-0.07296110227620.04110411187440.01075683935690.0728042109058-0.0606826781176-0.126902955641-0.00772498633309-0.417982237531-0.2398024221610.177925195731-0.351148615128-0.2475842595832.70913117903E-50.691937146972-0.0293319464156-0.001286562149930.429619907919-0.01186171417070.44930327438226.86297389345.0506202728-8.99089315405
120.03317670192120.05358539070170.02186028644320.07726185706810.1054860191430.06880952478170.1093949365170.2624807594230.157712221790.276103634006-0.344848889290.136202071663-0.3980785075120.0668911458362-0.0003072030893170.425377692342-0.0432883746983-0.03484547997870.373661987470.05417338858330.39617105204133.353549248622.9285443847-11.4109292315
13-0.00309838479841-0.00547004016203-0.02754092697220.0284350140247-0.0212572854583-0.02187523851710.1733899465290.0393477048186-0.170379829935-0.0768570399442-0.4392557874480.410456649559-0.228074019578-0.317829594552-0.0003347255524420.5913569365070.0534719197557-0.01963345594470.408193217443-0.06763750573470.33290376606630.707409366238.0056906846-14.693640793
14-0.00215357067749-0.003487192846320.002020939686380.01029543536510.002630027010340.0190231363243-0.218231142668-0.3869578639120.3850051246380.06171601897160.0307340923404-0.261402533125-0.2041893722380.1869232158117.03563142292E-50.879145799052-0.04176982180730.0004368646274940.4624881571620.01089509617290.66732534833836.905856066355.8821184755-14.9187488025
15-0.003982688232820.09661764636640.07294305718230.1220280093060.1133936659890.0782458732043-0.201994771075-0.2523974932140.1015862267160.6258145903930.0921658778081-0.409819835044-0.712615535474-0.5925653941095.2089240706E-50.697274948924-0.0285847170232-0.06572017513970.4144620757710.02645508990180.3610737705436.21490337138.5062376632-1.10954382037
16-0.000522531261412-0.000280955417249-0.01272858138930.04801856917910.04606143660660.0331679778672-0.202965860622-0.1849451957290.330214651521-0.117855273931-0.1110231758760.03106377119950.0004937912996040.330305841429-0.0002607338530050.381507208399-0.101581826870.04032895131470.3958081274530.02751040726870.27232547306541.455475405446.2328504195-11.1938121883
170.2946539153150.170604872905-0.04128027020890.0829233621549-0.02431449723690.134651858762-0.09717078532450.136922000002-0.0965251117525-0.4462661131740.330616590209-0.01072895459920.178838387383-0.05708084361230.0001876379941290.3353830860870.0100443392139-0.007276242480340.30439778327-0.01989863859260.33900734754114.6927444179-21.039174349-28.5789170354
180.3939771896960.572457319883-0.4411379709791.164227392090.3021196537320.902326886952-0.0369484328418-0.042867568372-0.0100587723632-0.110982023444-0.0139165830611-0.0226188965370.04420799378150.0277954139041-1.09698353341E-50.1805409532850.0125535384361-0.003049644612440.253457285865-0.005461425443590.25783196165420.2218651587-14.1147209992-22.3962425276
190.2122558127780.185191671215-0.1528575934630.0933970116469-0.02211797730760.040238969601-0.0246476059328-0.0248590569265-0.3519695856940.0152569301794-0.251622148759-0.02489498838490.1875830844560.0190242848644-0.02137687884140.4800203423730.02237409404890.02651999911860.180982038675-0.03098313155670.45088624121811.5813160449-37.7729456958-24.7997449863
200.761602263519-0.287410751299-0.9360720672210.5253952581650.2140094437840.874426987558-0.4136267895490.147970066577-0.298442751121-0.2086576720950.04959396864840.1775199593460.1042877208690.0752321336135-1.13998295806E-50.584287673625-0.08717358457110.02182629744740.5209225639830.002379698135910.568422958894-1.63936861456-40.7452483832-23.2783327005
210.01585888376780.0241102083223-0.128952039630.26959545603-0.2375735583510.402081306833-0.361515661109-0.151023739046-0.288833265893-0.457286522138-0.08672179259890.13233287219-0.00602744498343-0.09301314022323.42013788557E-50.483485999221-0.0197509696941-0.05612167299470.502984985241-0.08091987839510.55566274564-3.87354830123-43.687724639-28.634628665
221.171427088510.4171479453080.1784350774621.134008890990.19494922460.3084094485010.00146989137436-0.0645296484604-0.0273478185810.07247302533850.05762506965010.00234671672277-0.0798861968293-0.03978815997695.99340609973E-60.2523115079610.04185954585850.03756906211330.2885193956320.03293694939350.2499472554844.07331792813-4.34939580317-10.071304179
230.00722067892529-0.0369939373304-0.02182690727070.116299162146-0.05986335911530.0376843643459-0.21814920240.1269161411450.2705470468680.07923649169770.266617341557-0.02391437357190.02697516843380.1800653335510.00414010123570.20993002390.03522077716750.0428133262520.4208981469670.1739749462520.570043618751-14.2913071835-16.0231376553-14.1839416643
240.4079172204570.0754979672330.2522580606820.128329550117-0.265362906210.832787094664-0.330039678256-0.274588090732-0.2141745805160.05783929655060.1833894692370.1908713663950.178625528107-0.118869056423-4.27943539314E-50.288751407734-0.02243756134160.0413946315820.4017127380350.1378440470060.548324043642-5.545784625-38.8378051985-13.6354773553
250.1552996143560.0322854241576-0.1230944925790.338351330490.2011945916630.186769830793-0.0181784899267-0.146245333599-0.0188451094155-0.169657833247-0.02742715914290.048216269417-0.06242173005340.1479674355374.66343482824E-50.4756366333020.0223504049432-0.05110063277250.5248636552780.1721265129250.492525265818-5.33542165332-30.0178685619-16.362880575
260.6280148110820.106664818241-0.07350313280960.450096397096-0.3903369492690.246098168423-0.0958865622836-0.0482413788674-0.137146119580.172148896412-0.0696244662190.2045563230590.101531111891-0.110766331926-1.75318482024E-50.3264671903970.02152108972070.08890607129440.4376350969510.1022732082150.476254077589-9.95210852487-33.7193480496-7.02686152049
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 0 through 55 )AA0 - 551 - 56
22chain 'A' and (resid 56 through 114 )AA56 - 11457 - 115
33chain 'A' and (resid 115 through 182 )AA115 - 182116 - 183
44chain 'A' and (resid 183 through 269 )AA183 - 269184 - 258
55chain 'A' and (resid 270 through 270 )AA270259
66chain 'B' and (resid 0 through 5 )BC0 - 51 - 6
77chain 'B' and (resid 6 through 11 )BC6 - 117 - 12
88chain 'B' and (resid 12 through 19 )BC12 - 1913 - 20
99chain 'B' and (resid 20 through 30 )BC20 - 3021 - 31
1010chain 'B' and (resid 31 through 41 )BC31 - 4132 - 42
1111chain 'B' and (resid 42 through 51 )BC42 - 5143 - 52
1212chain 'B' and (resid 52 through 61 )BC52 - 6153 - 62
1313chain 'B' and (resid 62 through 71 )BC62 - 7163 - 72
1414chain 'B' and (resid 72 through 77 )BC72 - 7773 - 78
1515chain 'B' and (resid 78 through 90 )BC78 - 9079 - 91
1616chain 'B' and (resid 91 through 98 )BC91 - 9892 - 99
1717chain 'C' and (resid 2 through 17 )CD2 - 171 - 16
1818chain 'C' and (resid 18 through 102 )CD18 - 10217 - 101
1919chain 'C' and (resid 103 through 116 )CD103 - 116102 - 115
2020chain 'C' and (resid 117 through 165 )CD117 - 165116 - 161
2121chain 'C' and (resid 166 through 198 )CD166 - 198162 - 193
2222chain 'D' and (resid 1 through 106 )DE1 - 1061 - 106
2323chain 'D' and (resid 107 through 121 )DE107 - 121107 - 121
2424chain 'D' and (resid 122 through 159 )DE122 - 159122 - 159
2525chain 'D' and (resid 160 through 185 )DE160 - 185160 - 185
2626chain 'D' and (resid 186 through 240 )DE186 - 240186 - 240

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