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- PDB-8vq8: Immune receptor complex -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 8vq8
TitleImmune receptor complex
Components
  • (T cell receptor - LCK1-1 ...) x 2
  • H-2 class II histocompatibility antigen, A-B alpha chain
  • Nucleoprotein,H-2 class II histocompatibility antigen, A beta chain
KeywordsIMMUNE SYSTEM / peptide HLA complex / IMMUNE SYSTEM-VIRAL peptide complex
Function / homology
Function and homology information


positive regulation of antigen processing and presentation / positive regulation of alpha-beta T cell activation / positive regulation of T-helper 1 type immune response / antigen processing and presentation of peptide antigen / B cell affinity maturation / protein antigen binding / positive regulation of T cell differentiation / helical viral capsid / antigen processing and presentation / response to type II interferon ...positive regulation of antigen processing and presentation / positive regulation of alpha-beta T cell activation / positive regulation of T-helper 1 type immune response / antigen processing and presentation of peptide antigen / B cell affinity maturation / protein antigen binding / positive regulation of T cell differentiation / helical viral capsid / antigen processing and presentation / response to type II interferon / toxic substance binding / multivesicular body / MHC class II protein complex / antigen processing and presentation of exogenous peptide antigen via MHC class II / peptide antigen binding / cellular response to type II interferon / viral penetration into host nucleus / host cell / viral nucleocapsid / adaptive immune response / early endosome / lysosome / immune response / symbiont entry into host cell / ribonucleoprotein complex / external side of plasma membrane / ubiquitin protein ligase binding / host cell nucleus / structural molecule activity / Golgi apparatus / RNA binding / membrane / plasma membrane
Similarity search - Function
Influenza virus nucleoprotein (NP) / Influenza virus nucleoprotein / MHC class II, beta chain, N-terminal / Class II histocompatibility antigen, beta domain / Class II histocompatibility antigen, beta domain / MHC class II, alpha chain, N-terminal / Class II histocompatibility antigen, alpha domain / Class II histocompatibility antigen, alpha domain / MHC class II, alpha/beta chain, N-terminal / MHC classes I/II-like antigen recognition protein ...Influenza virus nucleoprotein (NP) / Influenza virus nucleoprotein / MHC class II, beta chain, N-terminal / Class II histocompatibility antigen, beta domain / Class II histocompatibility antigen, beta domain / MHC class II, alpha chain, N-terminal / Class II histocompatibility antigen, alpha domain / Class II histocompatibility antigen, alpha domain / MHC class II, alpha/beta chain, N-terminal / 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
H-2 class II histocompatibility antigen, A-B alpha chain / H-2 class II histocompatibility antigen, A beta chain / Nucleoprotein
Similarity search - Component
Biological speciesMus musculus (house mouse)
Influenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 Å
AuthorsChaurasia, P. / Littler, D.R. / La Gruta, N. / Rossjohn, J.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia) Australia
CitationJournal: To be published
Title: NP-LCK1-1TCR-MHC complex
Authors: Zhang, J.B. / Chaurasia, P. / Littler, D.R. / La Gruta, N. / Rossjohn, J.
History
DepositionJan 17, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 29, 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: T cell receptor - LCK1-1 TRAV6-5 alpha chain
B: T cell receptor - LCK1-1 TRBV1 Beta chain
C: H-2 class II histocompatibility antigen, A-B alpha chain
D: Nucleoprotein,H-2 class II histocompatibility antigen, A beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,31820
Polymers98,1664
Non-polymers1,15216
Water6,467359
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)197.604, 197.604, 79.331
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Space group name HallR3
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x+1/3,y+2/3,z+2/3
#5: -y+1/3,x-y+2/3,z+2/3
#6: -x+y+1/3,-x+2/3,z+2/3
#7: x+2/3,y+1/3,z+1/3
#8: -y+2/3,x-y+1/3,z+1/3
#9: -x+y+2/3,-x+1/3,z+1/3

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Components

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T cell receptor - LCK1-1 ... , 2 types, 2 molecules AB

#1: Protein T cell receptor - LCK1-1 TRAV6-5 alpha chain


Mass: 22889.146 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#2: Protein T cell receptor - LCK1-1 TRBV1 Beta chain


Mass: 27806.279 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)

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Protein , 2 types, 2 molecules CD

#3: Protein H-2 class II histocompatibility antigen, A-B alpha chain / IAalpha


Mass: 21204.674 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Expression tag on C terminal residue 181-188 / Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-Aa / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P14434
#4: Protein Nucleoprotein,H-2 class II histocompatibility antigen, A beta chain / Nucleocapsid protein / Protein N


Mass: 26266.168 Da / Num. of mol.: 1 / Fragment: 311-325
Source method: isolated from a genetically manipulated source
Details: Residue -25 to -11 (1-15 aligned sequence) QVYSLIRPNENPAHK- NP311-325, Flu peptide sequence. Residue GSGGSIEGRGGSGASGDS (16-34 aligned sequence) is unique peptide linker sequence from ...Details: Residue -25 to -11 (1-15 aligned sequence) QVYSLIRPNENPAHK- NP311-325, Flu peptide sequence. Residue GSGGSIEGRGGSGASGDS (16-34 aligned sequence) is unique peptide linker sequence from construct, not present in electron density.,Residue -25 to -11 (1-15 aligned sequence) QVYSLIRPNENPAHK- NP311-325, Flu peptide sequence. Residue GSGGSIEGRGGSGASGDS (16-34 aligned sequence) is unique peptide linker sequence from construct, not present in electron density.
Source: (gene. exp.) Influenza A virus, (gene. exp.) Mus musculus (house mouse)
Gene: NP, H2-Ab1, H2-iabeta / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P69296, UniProt: P14483

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Sugars , 1 types, 1 molecules

#6: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 2 types, 374 molecules

#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 359 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.22 Å3/Da / Density % sol: 61.76 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8.2 / Details: 0.1 M SPG pH 8.2, 5.0 %w/v PEG 1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95373 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 25, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 2.01→49.4 Å / Num. obs: 76994 / % possible obs: 99.9 % / Redundancy: 8.1 % / Biso Wilson estimate: 40.37 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.1159 / Rpim(I) all: 0.04327 / Rrim(I) all: 0.1238 / Net I/σ(I): 11
Reflection shellResolution: 2.01→2.05 Å / Redundancy: 8 % / Rmerge(I) obs: 1.296 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 4527 / CC1/2: 0.609 / Rpim(I) all: 0.454 / % possible all: 98.5

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.01→49.4 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 23.5118
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2151 3840 4.99 %
Rwork0.1866 73136 -
obs0.1881 76976 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 57.82 Å2
Refinement stepCycle: LAST / Resolution: 2.01→49.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6101 0 74 359 6534
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00726422
X-RAY DIFFRACTIONf_angle_d0.83598743
X-RAY DIFFRACTIONf_chiral_restr0.0571953
X-RAY DIFFRACTIONf_plane_restr0.00681141
X-RAY DIFFRACTIONf_dihedral_angle_d14.52922278
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.01-2.030.32851300.29762694X-RAY DIFFRACTION97.68
2.03-2.060.28891280.27542701X-RAY DIFFRACTION100
2.06-2.090.26731560.25892709X-RAY DIFFRACTION99.97
2.09-2.120.29151370.24212654X-RAY DIFFRACTION100
2.12-2.150.28651560.23462740X-RAY DIFFRACTION100
2.15-2.180.26371610.22832687X-RAY DIFFRACTION99.96
2.18-2.220.28451370.21682724X-RAY DIFFRACTION100
2.22-2.260.24151550.21212682X-RAY DIFFRACTION99.93
2.26-2.30.26111420.21772704X-RAY DIFFRACTION99.93
2.3-2.340.25651220.20862764X-RAY DIFFRACTION99.97
2.34-2.390.26351470.22262702X-RAY DIFFRACTION99.93
2.39-2.440.25881570.21582685X-RAY DIFFRACTION99.96
2.44-2.50.2581480.22192716X-RAY DIFFRACTION100
2.5-2.560.25671520.21562706X-RAY DIFFRACTION100
2.56-2.630.26741340.20692679X-RAY DIFFRACTION99.96
2.63-2.710.23231210.19932731X-RAY DIFFRACTION100
2.71-2.80.22261080.20522772X-RAY DIFFRACTION100
2.8-2.90.25471330.20242699X-RAY DIFFRACTION100
2.9-3.010.23531210.22746X-RAY DIFFRACTION99.97
3.01-3.150.23211540.20612711X-RAY DIFFRACTION100
3.15-3.320.22361480.19022706X-RAY DIFFRACTION100
3.32-3.520.22171630.18182682X-RAY DIFFRACTION100
3.52-3.80.1961550.17062721X-RAY DIFFRACTION100
3.8-4.180.16961660.16242683X-RAY DIFFRACTION100
4.18-4.780.1471250.14042707X-RAY DIFFRACTION100
4.78-6.020.1921670.1572702X-RAY DIFFRACTION100
6.02-49.40.21451170.18352729X-RAY DIFFRACTION99.82
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)
12.190057164772.994685888683.191904516994.636694693133.531652576356.10221557505-0.133888213072-0.3539829673460.0230076985461-0.196953218462-0.1483669868080.227355544906-0.364580112952-0.5981990046240.360871065350.1909524083080.05180960870470.01802890133390.45504716036-0.07083390686320.4092957178559.0413837772-66.5956747911-52.0446793353
27.966144345432.449359272460.7572935012480.7654784303430.1064745597781.520007952440.722620767233-0.3355819934772.1284463571-0.085422780702-0.183923032786-1.19105656443-0.5923315713060.525878384217-0.5763641733730.323583166078-0.04613447782540.0689548373190.609181363083-0.1549763223950.86099723168678.9250356933-59.0532660924-43.8537613753
33.702875143-0.3630493745180.1047839507952.032539263440.2007749134671.58398226912-0.0555600672284-0.266942047502-0.5327824908070.1246712621240.1227502059430.06258978233030.1629545356180.202084398475-0.01985374395680.2233418512420.06233802452310.03420447471160.3475490745140.03795645829210.33861243884762.0105062021-73.7567897593-44.3868261888
43.66279268875-5.037606690881.367973000497.13149373747-1.532345439351.02598930656-0.318275910497-0.532154978298-1.094575033750.604799551216-0.202145384659-0.4535351717270.617341983140.7902497315310.4834489862860.6405936791650.2982624595320.05411096082190.543325837570.008326587928231.6687818288568.0192757356-97.4374539765-52.4822151044
50.0978566882404-0.296812186993-0.5144924361992.214087257820.8881482501642.7855233989-0.152345543526-0.356284663244-1.687174639820.01621448487940.08255222948170.004274366507180.7604492755150.2476553458140.1730787042510.5971899655980.169724367603-0.01500671296840.533325549813-0.07094860090671.3835088026465.8062799453-95.0875426543-55.4848793397
65.92544012253-2.951984076340.780602029894.49042293758-0.4854141511511.849125753470.00969549573448-0.184777582872-0.2982942055950.08539733811810.1699112989390.454268225067-0.053777018551-0.247360495365-0.1651165128570.2000252972040.001755831127420.03562589047620.3430923780080.01947710693880.32178992593639.1161240396-53.5567541128-53.4889828394
71.17433681737-0.1921074101940.8261937588160.440123038489-0.9326660181012.64138819313-0.464181756167-0.2399865632280.224941976830.7350974046010.3543977272640.170367327877-1.56925228466-0.5873482304110.1462110496621.059095273870.296758968022-0.00908050847560.504978301803-0.03043268940730.40950413789628.9889412804-26.3222004525-63.4770911342
83.636137029070.735564684866-0.6523640781743.62951825292-2.142099860397.28680702887-0.1017696133180.3468234594690.213125167893-0.1105253548720.185318742236-0.0640604686234-0.326615301844-0.0751845820853-0.05798138714810.198215764188-0.05351585588810.03878908107920.315194050467-0.02319265871310.35570263005260.1293631621-44.3314761722-63.0492236284
94.94494166598-1.613796761430.7977032798114.81299228965-3.04217712535.82650486678-0.106062968136-0.3147122366530.2135516828150.3112535458710.1079048068220.054739267221-0.424869285411-0.20212341155-0.05718029677020.241411435273-0.02050456772360.03603913181180.29456318767-0.07013086623160.34542545951954.6360895017-46.5546896502-53.7111378539
102.13349274517-1.231501895980.2298383309783.12844874660.1762013082254.08728913359-0.457557725163-0.3320275544630.3407577408820.973631653989-0.202484793024-0.367015874805-1.607333226760.6764601222860.0272869769181.16069523052-0.0848056986482-0.302623815020.4088595035060.01258756452330.47341251002440.8192352353-23.1828397775-67.3046451848
110.8439169914870.103208233128-0.02799761609040.276266596109-0.4543559288050.761604206277-0.333884784131-0.6777589079060.7602335130711.293063294690.2455585069-0.101275631386-1.79290858971-0.2587253730060.1359549828422.299133195390.271043533654-0.5328514500260.510150206852-0.2062066936120.11516323519134.4073349386-17.1270578194-56.7122777544
124.96533173746-3.40291930363-1.559800613438.320471675566.631857002557.95676647493-0.5181712842690.3803038630241.449342477431.196276953530.273456393529-1.3618481009-0.4236618112321.20888094172-1.012730393691.25588884476-0.400432899122-0.4985903007450.8674134750040.2431756401970.90613623889150.7598106396-18.4068361765-69.1780469935
136.158445638446.21803815014-1.229326475378.4848704428-1.015139441252.05033635498-0.084097610892-0.214918319098-0.541837671143-0.0794137844487-0.00673455912182-0.5135084244330.03916017684320.2332814301830.1419919072970.1918090509920.09333147789670.04969861155240.389055516378-0.01821375909430.39070089068669.416067431-72.187253534-48.4818196314
145.07460988704-0.2080382900821.266654844234.81667598760.3999727534721.83177237870.08691625018720.795524781447-0.497570442751-0.3282515091120.0264338951538-0.1791570617830.205612003590.390235726737-0.117833753930.2728092023230.1047458801110.02376287039590.513138200596-0.1058521495630.32639900167466.470312092-73.427455333-60.6647108396
157.775319308025.550857833886.015925523937.889772323275.074132169784.867978097630.134890145421-0.0558434797860.634165350970.337537680529-0.0568250096127-0.0422608818992-0.07660314417420.541389838527-0.0698204347410.242973233745-0.01498023417020.07341395611760.456681445029-0.05314295898310.38282440047871.4098695323-58.5295911979-48.3206139805
163.81198411218-1.092966968770.03787052967565.330848769372.246495221463.299561651440.1608708018370.327565959257-0.7403084548930.392871242378-0.3975651981990.1285581337510.6076781750360.01963327604990.2776163723560.2792875410750.1211915273730.04636423046620.625561602868-0.1485188539710.6519730094583.0793880696-83.4727466112-54.4058081363
171.94453921965-2.441022837-1.98340175275.118708919132.111193448622.157251102410.315913143280.636649473726-0.377205188194-0.47293769234-0.448891552484-0.155623458857-0.1023484280010.131433648350.1061166371090.2546343130450.166834937344-0.0204010346240.63502648054-0.0773697772750.46045343955586.7307344258-77.6458992225-56.7051704721
185.91830539027-5.33482035601-1.869152456286.925553899324.487062612034.463894993010.2203584073720.722989551806-0.375650232602-0.272726995789-0.4530200741970.181029112976-0.215311300904-0.4216216197140.287649323860.2481396050930.06150999231720.01261926822380.464618570348-0.05048639852250.43262542094281.188893429-79.1296062605-56.9632112343
193.9262153279-1.28031974353-3.429850883952.638617462681.661996417493.6905931523-0.07213009735630.797471244986-0.563392006318-0.565448923934-0.5129710762960.5678568110980.1655637928650.2555489178950.5802177179180.4259475846490.277864138289-0.04342006484460.850698665808-0.241304065590.68960475358587.432808966-87.7829284709-64.5467002716
204.55408438936-4.08391452372-2.146235718773.913013846671.298700960072.41470870236-0.1795291543210.407203587957-0.3538637927490.3761391256990.184419560759-0.2915597812240.4375373560620.5221305485230.04904527625120.3167629131510.233833379770.01366077280270.818128023836-0.1705179183720.65032041216391.5360061455-86.0092628001-55.7028731626
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'D' and (resid -25 through -16 )DP-25 - -161 - 10
22chain 'D' and (resid -15 through 5 )DP-15 - 511 - 18
33chain 'D' and (resid 6 through 120 )DP6 - 12019 - 118
44chain 'D' and (resid 121 through 142 )DP121 - 142119 - 126
55chain 'D' and (resid 143 through 185 )DP - Q143 - 301127
66chain 'A' and (resid 1 through 112 )AA1 - 1121 - 98
77chain 'A' and (resid 113 through 204 )AA113 - 20499 - 190
88chain 'B' and (resid 1 through 107 )BF1 - 1071 - 94
99chain 'B' and (resid 108 through 122 )BF108 - 12295 - 109
1010chain 'B' and (resid 123 through 200 )BF123 - 200110 - 187
1111chain 'B' and (resid 201 through 213 )BF201 - 213188 - 200
1212chain 'B' and (resid 214 through 243 )BF214 - 243201 - 229
1313chain 'C' and (resid 1 through 20 )CI1 - 201 - 20
1414chain 'C' and (resid 21 through 57 )CI21 - 5721 - 57
1515chain 'C' and (resid 58 through 78 )CI58 - 7858 - 78
1616chain 'C' and (resid 79 through 112 )CI79 - 11279 - 112
1717chain 'C' and (resid 113 through 125 )CI113 - 125113 - 125
1818chain 'C' and (resid 126 through 148 )CI126 - 148126 - 148
1919chain 'C' and (resid 149 through 168 )CI149 - 168149 - 168
2020chain 'C' and (resid 169 through 186 )CI169 - 186169 - 186

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