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- PDB-9bys: Structure of human MAIT BV28 TCR in complex with human MR1-5-OP-RU -

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Basic information

Entry
Database: PDB / ID: 9bys
TitleStructure of human MAIT BV28 TCR in complex with human MR1-5-OP-RU
Components
  • Beta-2-microglobulin
  • Major histocompatibility complex class I-related gene protein
  • TCR alpha chain
  • TCR beta chain
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 / MHC class II protein complex / negative regulation of forebrain neuron differentiation / 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 / positive regulation of T cell activation / peptide antigen binding / positive regulation of receptor-mediated endocytosis / negative regulation of neurogenesis / 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 / defense response to Gram-negative bacterium / protein homotetramerization / 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 / lysosomal membrane / innate immune response / 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: 3.1 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
DepositionMay 24, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 11, 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: Major histocompatibility complex class I-related gene protein
AAAB: TCR beta chain
AAAC: TCR alpha chain
AAAD: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,9158
Polymers94,3094
Non-polymers6074
Water1,874104
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)111.350, 111.350, 206.460
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

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Protein , 4 types, 4 molecules AAAABAAACAAAD

#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 TCR beta chain


Mass: 27934.328 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)
#3: Protein TCR alpha chain


Mass: 22783.283 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)
#4: Protein Beta-2-microglobulin


Mass: 11879.356 Da / Num. of mol.: 1 / Fragment: UNP residues 21-119
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

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Non-polymers , 3 types, 108 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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / 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: 3.39 Å3/Da / Density % sol: 63.75 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: PEG3350, Na-acetate, BTP

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95371 Å
DetectorType: APEX II CCD / Detector: CCD / Date: May 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95371 Å / Relative weight: 1
ReflectionResolution: 3.1→46.83 Å / Num. obs: 24316 / % possible obs: 99.9 % / Redundancy: 4 % / Biso Wilson estimate: 64.36 Å2 / CC1/2: 0.95 / Net I/σ(I): 6.9
Reflection shellResolution: 3.1→3.2 Å / Num. unique obs: 2385 / CC1/2: 0.8

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→46.83 Å / SU ML: 0.3635 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.1191
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2524 1219 5.01 %
Rwork0.222 23090 -
obs0.2235 24309 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 77.49 Å2
Refinement stepCycle: LAST / Resolution: 3.1→46.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5730 0 40 104 5874
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025928
X-RAY DIFFRACTIONf_angle_d0.48658059
X-RAY DIFFRACTIONf_chiral_restr0.0413873
X-RAY DIFFRACTIONf_plane_restr0.00371053
X-RAY DIFFRACTIONf_dihedral_angle_d15.57462094
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.220.31051500.28882486X-RAY DIFFRACTION99.96
3.22-3.370.30221340.27872528X-RAY DIFFRACTION100
3.37-3.550.29781340.252506X-RAY DIFFRACTION100
3.55-3.770.26571450.22112514X-RAY DIFFRACTION99.96
3.77-4.060.23361240.20992540X-RAY DIFFRACTION100
4.06-4.470.19791470.18482547X-RAY DIFFRACTION100
4.47-5.120.19821420.16912560X-RAY DIFFRACTION100
5.12-6.440.23421200.21972625X-RAY DIFFRACTION100
6.44-46.830.29891230.24772784X-RAY DIFFRACTION99.79
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.55873670217-0.3684793422840.3027890190172.29038176623-0.1023555571141.917388947050.0633070788513-0.152910110618-0.193565236699-0.05203131160790.03316712096250.219285203190.23407095364-0.481257775636-0.08686568247930.362246274943-0.108416590624-0.004166573359340.454307481120.0398845326370.319199268577116.69275090912.1213876087224.57197713
21.6558093282-0.80477365196-0.8092345641742.362357952580.5247753815221.518755715660.00688496321751-0.219538398055-0.2242341037340.1439046718140.185922535211-0.2861516250930.603571530853-0.0652207076085-0.1419894358150.52962220289-0.0508083723915-0.1517671724570.3762202249160.1110483716720.476876498575137.270047344-4.38316193485222.49318735
33.304447801110.3624734916320.6130342640122.60535048091-0.4264433814431.886968722520.2746638059710.447214018430.00479141044011-0.514803249556-0.360354436415-0.00782347551626-0.05089269998180.05323283262760.03197954337550.7408368298410.0513697868085-0.2061749450280.369678199765-0.006878278051540.534583197373142.259140986-10.0050205795209.630431182
40.0850052193619-0.0667173757226-0.0495381706858-0.133085195205-0.039216677505-0.0335377666031-0.593573833405-0.218667126028-0.2884697175730.635724080754-0.06862608232790.724879224405-0.379275863235-1.19603141980.1316992846180.8455677545240.061426574540.4448218776261.40870682087-0.02964202963141.073950553196.4951475130.8271601237251.16937056
51.901510537090.149439578804-1.220662699373.784303570520.4952186320041.01470531713-0.494429019110.284395388981-0.2181697479960.152383260512-0.2586064848031.12192177345-0.3336660737850.558198024980.4247494282550.458851436256-0.04920834483440.1573930037630.8106499299490.02184377575450.741528169672104.17448456827.8236916404239.954706996
61.034728655460.2498602471390.1752773579051.639108176260.5331132986271.61732476608-0.0836271837648-0.312919585621-0.3338967113570.385961417389-0.01995659233120.4184935208590.242630436274-0.5704559822940.08599446473530.564428852351-0.1184897400050.2416182088720.9347053718190.02929837035520.689714437196105.11308784225.0559261095245.828550892
71.189079865491.05569301239-0.3547146667221.68323229971-0.1655264109820.7070059203180.148805898803-1.035910387381.130833959520.0112382936621-0.03321622811220.746888748070.0155356429625-0.452475490520.08080445995370.9075978312710.2644151763130.2923538928941.40252113325-0.3953414139441.27928156766101.68236666651.0670380397259.857753748
83.46713344759-0.298457778711.130143383083.693301494970.5701366882393.524333237980.828323103466-0.315678476463-0.2922713146080.6033386197590.2541334743190.138429059049-0.169232097497-0.146692786616-0.4639186023950.769150275683-0.1031357413470.3392145812881.61582958539-0.2177125378911.4532232226990.481310243939.6033135864259.70759398
94.08800193753-0.9462265382432.646546166791.042241879350.5375564235913.70698150692-0.384821534867-0.5011613156680.8452140779240.05820789218330.1593714142660.1188629953310.781669562889-0.50136625655-0.06130433446870.8372165132830.1423013452750.3767886879341.54833902522-0.4693802352761.6061845174288.969423406245.3260925081265.283006226
101.29827165460.656460177413-0.07643351855253.995662809610.3687832712562.33195871592-0.133951289472-0.3481490480560.03554593321370.1630431185790.190581471848-0.5200894192590.347463803018-0.377689851528-0.0197567652720.50463950714-0.0397515938784-0.02740499228620.487157786853-0.1019145430190.430899891178124.53871016943.2241836168245.733877197
111.844225162230.4339444533540.2022623968663.096867793360.3332485656791.114702787320.0334343688107-0.3556804779320.08753652425690.928058475876-0.126041179656-0.004952154501560.215271065846-0.02923977097450.07686445754960.560227630807-0.0576283065596-0.003411870704410.432026136974-0.01808914357810.203598197156123.45668819434.3487470663239.57206071
120.5218621604730.7928658240680.5725984313181.477228352970.3897246848961.470919196610.398916326549-0.6177759846680.242250481148-0.202222954329-0.3088132600690.25248588842-0.460048449815-0.4783104667910.06939105609940.4747853961310.02932174696510.04654691777360.589378253381-0.03236748051660.415138874451115.84242186337.4713449345236.343826357
132.10825320016-0.945366549644-0.0320085805133.915759159260.3949035466261.94885674460.1716168255620.5265699954160.216087202739-0.149058382645-0.2491727449340.126264638128-0.1963286767710.0797813813694-0.02306296448190.424137606625-0.007497964765640.001068831132150.321577905765-0.007539921004770.338392547475126.20807765740.1487983229233.085914208
141.92787360149-1.62864595734-0.3295993518793.91231538739-0.1301475555291.438114307860.0964337513085-0.1140429355070.529791954874-0.385239973148-0.006394719148250.229600554609-0.315848823095-0.4981995613060.03557376240420.5405473250250.1350289320910.0196141395010.531769615187-0.118768364350.557306770342117.97061137245.3231099171239.896972732
152.138879247370.1359135823420.9466974022354.068969376971.834795975681.10541909585-0.119955921418-0.1858636361480.3903503019980.3353626078680.06692213033910.0212360685475-0.0606335540008-0.3440180565750.002743837960220.6733291241380.05535708990180.1820183313920.512261919096-0.09349595228660.383303516816119.31065169445.201715758244.956067588
160.831470142836-0.724532286362-0.1889632615260.7824540412550.4348993950350.5804618858330.318048560198-0.39743766780.8258785099560.140942043741-1.38195648612-0.5158493800660.825780690109-0.3308346308290.5052989875381.183624436480.1303149272380.1485471522361.45611551132-0.4933238591861.6108327008114.13980303666.353879143257.96268167
170.0651750445223-0.0515864769704-0.1397508106350.05922812379810.1999234850650.687098876812-0.136628048257-0.4944140667240.2987201988841.22923227577-0.0150690329293-0.49339780728-0.002022069880610.243025344351-0.0393450283191.354754096360.4144215142450.04039807626781.657712238350.1208478113471.16976001918117.78580435356.6163449171266.439404414
182.842681900190.906100114516-0.9486425033251.938087065270.7028324739920.8953523667170.295814327421-0.04062958967191.01800241021-0.4320656096430.06676422010580.4540202967780.0842494676313-0.796150405598-0.3523490668731.003357993020.342427250571-0.01879696865410.962177098702-0.2927228056071.29033661182110.4193195461.6918046867251.917517449
19-0.01762720974020.0266445823557-0.1040586224240.0129815298060.103103100325-0.01803769448960.177300149844-0.3105740040670.08900048136740.331066042708-0.27310730919-0.384796457776-0.2863133270210.3580469447620.01737114142551.099508216870.184536044092-0.3788286202751.34444931632-0.3232013289871.21370687045120.31188122665.6396923831263.554550946
202.803584472760.436331931384-0.6832757642960.2634344085810.4699201048241.88055887501-0.594067389341-0.03181244296720.242763136605-0.0510223914792-0.0757155049320.227116432637-0.547962451671-0.6434533773240.4034399473730.869818151265-0.280728123187-0.2682687738040.659493595202-0.06997936900170.866403507787111.874761054-1.25369675073209.341727767
210.41699712110.650769681878-0.2983138984870.8357678347630.002800621752191.492385826860.02600947673470.104841915068-0.5074579361220.614283933579-0.2950833263060.0313847342930.5015929446880.1530924427030.1481323098110.77364192001-0.166153675947-0.09547601361720.4321793669080.01984528418980.834736667606127.206622205-17.2809250856219.891205165
221.62476189542-1.523502981690.7103111657958.52846361082-2.072052018791.559335237980.9297892263180.10341674738-1.135408974810.4752858289720.2263607518191.09865017905-0.28948594419-1.87842096817-0.5160520023220.693764690271-0.648039752335-0.2353687717130.2943041238280.1447595476091.14573092206113.123537448-12.5865099956218.691891915
230.009942556876710.01499355740870.04819333244850.1165564569910.00555789378065-0.009891732046220.803414511691-0.612031721666-0.839692603120.3349624254640.1194392745680.7297503381580.82579803327-0.776806718618-0.2819119525131.35023102075-0.317293870691-0.2363530073920.7194969705610.1388511096321.45419111314115.626726949-21.557062809225.090219231
240.370768560913-1.23174877692-0.09593621937013.18466684211-0.272897993570.8788571222720.135785202276-0.114764178325-0.5059970207820.501638319359-0.118984638061-0.1934547692460.236449886385-0.1783612220960.01690615550010.669292330644-0.207884230137-0.04104803110990.5121474482290.1288067810160.709918273801121.55480962-12.1172591573221.336484115
253.38207897303-3.029371218821.39231801575.34136186271-1.557101298332.736272826840.999738065310.506748223044-1.00345710578-0.438701889326-0.08365625748460.7523208444220.5787014467540.467933967139-0.503649709010.841217855026-0.200451168988-0.2948933909590.671861397781-0.1533862325981.25543079879116.674600844-17.884060185212.723301406
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 158 )AA0 - 1581 - 159
22chain 'A' and (resid 159 through 205 )AA159 - 205160 - 204
33chain 'A' and (resid 206 through 270 )AA206 - 270205 - 267
44chain 'D' and (resid 3 through 25 )AAABC3 - 251 - 23
55chain 'D' and (resid 26 through 37 )AAABC26 - 3724 - 35
66chain 'D' and (resid 38 through 107 )AAABC38 - 10736 - 105
77chain 'D' and (resid 108 through 211 )AAABC108 - 211106 - 169
88chain 'D' and (resid 212 through 221 )AAABC212 - 221170 - 179
99chain 'D' and (resid 222 through 238 )AAABC222 - 238180 - 196
1010chain 'C' and (resid 1 through 17 )AAACD1 - 171 - 17
1111chain 'C' and (resid 18 through 37 )AAACD18 - 3718 - 37
1212chain 'C' and (resid 38 through 52 )AAACD38 - 5238 - 52
1313chain 'C' and (resid 53 through 75 )AAACD53 - 7553 - 75
1414chain 'C' and (resid 76 through 91 )AAACD76 - 9176 - 91
1515chain 'C' and (resid 92 through 116 )AAACD92 - 11692 - 116
1616chain 'C' and (resid 117 through 140 )AAACD117 - 140117 - 130
1717chain 'C' and (resid 141 through 150 )AAACD141 - 150131 - 140
1818chain 'C' and (resid 151 through 173 )AAACD151 - 173141 - 163
1919chain 'C' and (resid 174 through 194 )AAACD174 - 194164 - 173
2020chain 'B' and (resid 0 through 5 )AAADE0 - 51 - 6
2121chain 'B' and (resid 6 through 30 )AAADE6 - 307 - 31
2222chain 'B' and (resid 31 through 41 )AAADE31 - 4132 - 42
2323chain 'B' and (resid 42 through 51 )AAADE42 - 5143 - 52
2424chain 'B' and (resid 52 through 77 )AAADE52 - 7753 - 78
2525chain 'B' and (resid 78 through 98 )AAADE78 - 9879 - 99

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