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- PDB-9ngt: Crystal structure of CRBN-DDB1 and FPFT-2216 in complex with mTOR -

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Basic information

Entry
Database: PDB / ID: 9ngt
TitleCrystal structure of CRBN-DDB1 and FPFT-2216 in complex with mTOR
Components
  • DNA damage-binding protein 1
  • Protein cereblon
  • Serine/threonine-protein kinase mTOR
KeywordsDNA Binding Protein/Transferase / Ternary complex / Molecular glue degrader / neosubstrate / DNA Binding Protein-Transferase complex
Function / homology
Function and homology information


RNA polymerase III type 2 promoter sequence-specific DNA binding / RNA polymerase III type 1 promoter sequence-specific DNA binding / positive regulation of cytoplasmic translational initiation / regulation of locomotor rhythm / T-helper 1 cell lineage commitment / positive regulation of pentose-phosphate shunt / positive regulation of wound healing, spreading of epidermal cells / TORC2 signaling / TORC2 complex / regulation of membrane permeability ...RNA polymerase III type 2 promoter sequence-specific DNA binding / RNA polymerase III type 1 promoter sequence-specific DNA binding / positive regulation of cytoplasmic translational initiation / regulation of locomotor rhythm / T-helper 1 cell lineage commitment / positive regulation of pentose-phosphate shunt / positive regulation of wound healing, spreading of epidermal cells / TORC2 signaling / TORC2 complex / regulation of membrane permeability / cellular response to leucine starvation / negative regulation of lysosome organization / heart valve morphogenesis / TFIIIC-class transcription factor complex binding / TORC1 complex / voluntary musculoskeletal movement / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / negative regulation of monoatomic ion transmembrane transport / calcineurin-NFAT signaling cascade / RNA polymerase III type 3 promoter sequence-specific DNA binding / positive regulation of keratinocyte migration / regulation of osteoclast differentiation / regulation of lysosome organization / MTOR signalling / cellular response to L-leucine / energy reserve metabolic process / regulation of autophagosome assembly / Energy dependent regulation of mTOR by LKB1-AMPK / cellular response to nutrient / Amino acids regulate mTORC1 / TORC1 signaling / ruffle organization / serine/threonine protein kinase complex / cellular response to methionine / positive regulation by virus of viral protein levels in host cell / negative regulation of cell size / positive regulation of ubiquitin-dependent protein catabolic process / spindle assembly involved in female meiosis / cellular response to osmotic stress / epigenetic programming in the zygotic pronuclei / negative regulation of protein localization to nucleus / anoikis / inositol hexakisphosphate binding / cardiac muscle cell development / UV-damage excision repair / negative regulation of calcineurin-NFAT signaling cascade / regulation of myelination / positive regulation of transcription by RNA polymerase III / biological process involved in interaction with symbiont / regulation of mitotic cell cycle phase transition / WD40-repeat domain binding / negative regulation of macroautophagy / Cul4A-RING E3 ubiquitin ligase complex / Cul4-RING E3 ubiquitin ligase complex / Macroautophagy / positive regulation of myotube differentiation / regulation of cell size / Cul4B-RING E3 ubiquitin ligase complex / ubiquitin ligase complex scaffold activity / Constitutive Signaling by AKT1 E17K in Cancer / positive regulation of actin filament polymerization / germ cell development / TOR signaling / negative regulation of reproductive process / negative regulation of developmental process / behavioral response to pain / mTORC1-mediated signalling / locomotory exploration behavior / oligodendrocyte differentiation / positive regulation of oligodendrocyte differentiation / cullin family protein binding / viral release from host cell / positive regulation of translational initiation / CD28 dependent PI3K/Akt signaling / HSF1-dependent transactivation / regulation of macroautophagy / positive regulation of Wnt signaling pathway / 'de novo' pyrimidine nucleobase biosynthetic process / response to amino acid / ectopic germ cell programmed cell death / positive regulation of epithelial to mesenchymal transition / vascular endothelial cell response to laminar fluid shear stress / positive regulation of lipid biosynthetic process / heart morphogenesis / cellular response to nutrient levels / negative regulation of protein-containing complex assembly / neuronal action potential / positive regulation of viral genome replication / regulation of cellular response to heat / proteasomal protein catabolic process / positive regulation of lamellipodium assembly / cardiac muscle contraction / T cell costimulation / phagocytic vesicle / positive regulation of stress fiber assembly / cytoskeleton organization / endomembrane system / positive regulation of gluconeogenesis / negative regulation of insulin receptor signaling pathway / negative regulation of autophagy
Similarity search - Function
Domain of unknown function DUF3385, target of rapamycin protein / Serine/threonine-protein kinase mTOR domain / Domain of unknown function / FKBP12-rapamycin binding domain / Serine/threonine-protein kinase TOR / FKBP12-rapamycin binding domain superfamily / FKBP12-rapamycin binding domain / Rapamycin binding domain / Serine/threonine-protein kinase ATR-like, HEAT repeats / Yippee/Mis18/Cereblon ...Domain of unknown function DUF3385, target of rapamycin protein / Serine/threonine-protein kinase mTOR domain / Domain of unknown function / FKBP12-rapamycin binding domain / Serine/threonine-protein kinase TOR / FKBP12-rapamycin binding domain superfamily / FKBP12-rapamycin binding domain / Rapamycin binding domain / Serine/threonine-protein kinase ATR-like, HEAT repeats / Yippee/Mis18/Cereblon / Yippee zinc-binding/DNA-binding /Mis18, centromere assembly / CULT domain / CULT domain profile. / Lon N-terminal domain profile. / Lon protease, N-terminal domain / Lon protease, N-terminal domain superfamily / ATP-dependent protease La (LON) substrate-binding domain / Found in ATP-dependent protease La (LON) / : / FATC domain / PIK-related kinase, FAT / FAT domain / FATC / FATC domain / PIK-related kinase / FAT domain profile. / FATC domain profile. / RSE1/DDB1/CPSF1 second beta-propeller / Cleavage/polyadenylation specificity factor, A subunit, C-terminal / Cleavage/polyadenylation specificity factor, A subunit, N-terminal / : / CPSF A subunit region / RSE1/DDB1/CPSF1 first beta-propeller / PUA-like superfamily / Phosphatidylinositol 3- and 4-kinases signature 1. / Phosphatidylinositol 3/4-kinase, conserved site / Phosphatidylinositol 3- and 4-kinases signature 2. / Phosphatidylinositol 3-/4-kinase, catalytic domain superfamily / Phosphoinositide 3-kinase, catalytic domain / Phosphatidylinositol 3- and 4-kinase / Phosphatidylinositol 3- and 4-kinases catalytic domain profile. / Phosphatidylinositol 3-/4-kinase, catalytic domain / Armadillo-like helical / Tetratricopeptide-like helical domain superfamily / Armadillo-type fold / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Protein kinase-like domain superfamily
Similarity search - Domain/homology
: / Serine/threonine-protein kinase mTOR / DNA damage-binding protein 1 / Protein cereblon
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsPetzold, G. / Trenh, P. / Bunker, R.D. / Tsai, J.H.C.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Science / Year: 2025
Title: Mining the CRBN target space redefines rules for molecular glue-induced neosubstrate recognition.
Authors: Petzold, G. / Gainza, P. / Annunziato, S. / Lamberto, I. / Trenh, P. / McAllister, L.A. / DeMarco, B. / Schwander, L. / Bunker, R.D. / Zlotosch, M. / SriRamaratnam, R. / Gilberto, S. / ...Authors: Petzold, G. / Gainza, P. / Annunziato, S. / Lamberto, I. / Trenh, P. / McAllister, L.A. / DeMarco, B. / Schwander, L. / Bunker, R.D. / Zlotosch, M. / SriRamaratnam, R. / Gilberto, S. / Langousis, G. / Donckele, E.J. / Quan, C. / Strande, V. / De Donatis, G.M. / Alabi, S.B. / Alers, J. / Matysik, M. / Staehly, C. / Dubois, A. / Osmont, A. / Garskovas, M. / Lyon, D. / Wiedmer, L. / Oleinikovas, V. / Lieberherr, R. / Rubin, N.T. / Lam, D.T. / Lucas, X. / Liardo, E. / Widlund, N.I. / Ritzen, A. / Caceres, R.M. / Vigil, D. / Tsai, J. / Wallace, O. / Peluso, M. / Sadok, A. / Tiedt, R. / Paterson, A.M. / Zarayskiy, V. / Fasching, B. / Bonenfant, D. / Warmuth, M. / Castle, J.C. / Townson, S.A.
History
DepositionFeb 22, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 9, 2025Provider: repository / Type: Initial release
Revision 1.1Jul 16, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA damage-binding protein 1
B: Protein cereblon
C: Serine/threonine-protein kinase mTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)189,8625
Polymers189,5053
Non-polymers3582
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: fluorescence resonance energy transfer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)183.176, 81.213, 99.020
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab

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Components

#1: Protein DNA damage-binding protein 1 / DDB p127 subunit / DNA damage-binding protein a / DDBa / Damage-specific DNA-binding protein 1 / ...DDB p127 subunit / DNA damage-binding protein a / DDBa / Damage-specific DNA-binding protein 1 / HBV X-associated protein 1 / XAP-1 / UV-damaged DNA-binding factor / UV-damaged DNA-binding protein 1 / UV-DDB 1 / XPE-binding factor / XPE-BF / Xeroderma pigmentosum group E-complementing protein / XPCe


Mass: 127097.469 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DDB1, XAP1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q16531
#2: Protein Protein cereblon


Mass: 50603.676 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CRBN, AD-006 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q96SW2
#3: Protein Serine/threonine-protein kinase mTOR / FK506-binding protein 12-rapamycin complex-associated protein 1 / FKBP12-rapamycin complex- ...FK506-binding protein 12-rapamycin complex-associated protein 1 / FKBP12-rapamycin complex-associated protein / Mammalian target of rapamycin / mTOR / Mechanistic target of rapamycin / Rapamycin and FKBP12 target 1 / Rapamycin target protein 1 / Tyrosine-protein kinase mTOR


Mass: 11803.489 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MTOR, FRAP, FRAP1, FRAP2, RAFT1, RAPT1 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P42345, non-specific serine/threonine protein kinase, non-specific protein-tyrosine kinase
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-A1BC8 / (3S)-3-[(4M)-4-(4-methoxythiophen-3-yl)-1H-1,2,3-triazol-1-yl]piperidine-2,6-dione


Mass: 292.314 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H12N4O3S / Feature type: SUBJECT OF INVESTIGATION
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: 1.94 Å3/Da / Density % sol: 36.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 70 mM MES pH 6.0, 1.8-3.2 % (w/v) PEG 3,000, and 13-24 % (w/v) PEG 200

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.96546 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 8, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96546 Å / Relative weight: 1
ReflectionResolution: 2.61→74.24 Å / Num. obs: 30713 / % possible obs: 96.5 % / Redundancy: 11 % / CC1/2: 0.997 / Rmerge(I) obs: 0.153 / Net I/σ(I): 10.9
Reflection shellResolution: 2.95→3.05 Å / Num. unique obs: 1372 / CC1/2: 0.438

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Processing

Software
NameVersionClassification
PHENIXdev_5430refinement
DIALSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.95→43.78 Å / SU ML: 0.3758 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.243
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2603 1530 5.16 %
Rwork0.2314 28138 -
obs0.2329 29668 93.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 85.42 Å2
Refinement stepCycle: LAST / Resolution: 2.95→43.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9998 0 21 0 10019
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.010710221
X-RAY DIFFRACTIONf_angle_d1.321613831
X-RAY DIFFRACTIONf_chiral_restr0.08241550
X-RAY DIFFRACTIONf_plane_restr0.00651790
X-RAY DIFFRACTIONf_dihedral_angle_d16.83563817
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.95-3.050.4182730.34761372X-RAY DIFFRACTION50.83
3.05-3.150.35581210.31052063X-RAY DIFFRACTION76.58
3.15-3.280.34191450.28572587X-RAY DIFFRACTION95.13
3.28-3.430.27471240.26982714X-RAY DIFFRACTION100
3.43-3.610.31011510.26372722X-RAY DIFFRACTION100
3.61-3.840.27021440.24582718X-RAY DIFFRACTION100
3.84-4.130.23311460.232747X-RAY DIFFRACTION100
4.13-4.550.24191570.20192739X-RAY DIFFRACTION100
4.55-5.20.24451510.18982759X-RAY DIFFRACTION100
5.21-6.550.25411520.23182793X-RAY DIFFRACTION100
6.56-43.780.22331660.21092924X-RAY DIFFRACTION99.97
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)
13.42384049227111.0634216087112-0.244944035556023.13691396168480.14946021362362.35465687268550.21904520188999-0.405194031912380.311751869825890.58812358447054-0.20698388026602-0.31129206062086-0.330380188596080.2406919944848-0.0179256207233280.59040047819233-0.10611214540814-0.0927729743933540.44616920063480.0303813932732790.46865336200813-22.10625965051528.285571277503-10.742928152774
22.3612613370959-0.47417664298435-0.653406738913272.42519060971360.272477198097891.87555369134320.169338821634720.0570394186354480.477613050902690.0032051259176148-0.084636309703543-0.25047174843906-0.29511257082556-0.049458012202798-0.0646498607370250.35394673898935-0.083837290137004-0.0449390149156180.321081153238670.105317421325730.68360099577414-20.3671715980736.38123393556-30.488531958229
34.64368566696091.13839548321931.53450743047293.77162594533440.746003097383712.13229262091190.1118711819424-0.050860292458483-0.185611932021050.23454897968175-0.087111322992076-0.545042582794430.225628765044660.12677872797487-0.0940218316172380.464391216926410.042287073939011-0.0224117302067810.322914723209180.1204945581070.58864483345204-21.3316235961231.0839725906649-27.067752228775
45.41771214539310.23727596867745-0.187377379338724.8881036671873-0.648098272884212.4077654799659-0.0471657052269020.22878300448834-0.41936543117779-0.102425994952140.0126820343800690.161885122392830.35328338718291-0.43414440403199-0.0262005262126450.47092129382954-0.0550633891416370.0234114229553380.35582635111716-0.0339901229576120.51379256211553-41.092988166217-6.7783614988297-34.436050381369
53.71057990885390.44571107879277-0.147900100653083.4952123412164-0.415720903211663.73478184262120.18855948250286-0.34782032489651-0.196416900311850.55808381561724-0.237741970965020.77379296449520.29911511050466-0.80962035749265-0.0728689088130420.5769883474638-0.123106842264740.156247266668220.565614564117570.0313421700328890.56249281590436-48.1606436317114.7226865478338-13.023269561771
63.73006163571450.77868571173824-0.948821591175356.47087049498050.132048460244567.53311401957320.0021654021729897-0.60467701277924-0.170440691216011.0418977846916-0.011520658523798-0.164662408545340.285114026626720.536278194514640.073057591368590.89192225449483-0.0979660685663480.0933448959476290.76659127362312-0.0649495791594920.39642324709257-35.14289755500415.9919473513184.3504864129166
73.0101923755069-3.736833457375-1.32454058928235.08971795389830.429335240030582.13194226158050.3635355744697-0.726809070284082.77619130330230.071513379240925-0.52911916754434-0.36789398457129-1.42392399824450.120325183349180.193376373176150.214890270034050.74661473349920.305146801026870.74878349400815-0.505637118623242.389824749354-75.48123470640734.699897322917-23.664949424026
82.8336480781053-1.8087079575342-1.06442632628461.2977910368233-0.0728887658562522.03584837864710.1516357273902-0.480706188422130.75186571239297-0.28090975408923-0.170962276997560.46578847309962-0.501205410517080.14085870057838-0.121785937558410.835175193358460.2308353295010.312402694915121.2278510661687-0.229363787525641.7636816489051-76.8831662395533.172795821041-22.513244803944
97.87426266599942.4134513131385-1.30325409561384.0953347994614-0.731101543275548.5905470437439-0.359360728239180.751525459279050.072259738189714-0.24840870086709-0.218043466706480.11364908847382-0.078436678806470.231132765790860.385979492312660.585430045127580.0345425555971910.0439673792808040.470656949771120.121939264059360.87595852558284-39.38688961007722.035464897481-34.17909194601
103.58589453041720.0826050951900442.66491925092950.82099358608551-0.111358331849332.9900694085417-0.171310431136120.126075349619290.24818962425187-0.17299421077234-0.131271621996380.23728972486303-0.24159571334436-0.23488697452480.208970179403560.427916026363490.0168517103620250.015570405454530.387501299175770.0146405710487670.57415319901938-57.82052700935116.626106982523-37.004362459983
114.63012714526070.458877181695112.2606625942164.9576279297712-2.04276233537386.28055293043050.20606229737083-0.062040950355210.34069813273350.21501234650275-0.0423732769464420.38742920489435-0.068491337619398-0.434610590525720.0402188653165360.28632021425703-0.013218704414540.0744689534494630.33906855046767-0.144566221063660.72057625232578-77.75035367178716.514516753258-49.576895972392
124.3537553858276-0.36944455009038-4.39174204967671.67615180945730.0703228932619674.7549643439454-0.398230632421171.2060066273205-0.276651376613180.886412056143760.217677261230820.72998591547351-1.9252539408283-1.4119576239628-0.225538628825961.1447744438516-0.126883163533340.270466603780751.20390812920490.0744119377234650.93977613854821-112.411429603724.368243706509-41.663886118603
133.40049016321783.34597345674570.812851472812325.5954107320762-1.32662817309553.57227633044210.57002014185929-1.63210625068980.525470106839461.17440387371080.21320046726972-0.50760366954116-2.14299128363940.86722136819865-0.0855245773501481.2642867078186-0.0582892746620850.150882520841740.992345515151310.0231228811484440.92603076846614-105.7032717555727.067054613318-37.283965023809
142.92548774058420.97488862288003-5.04326660720725.7556780586911-0.952163411892889.14767732856310.83928277743144-1.4420538028826-0.703143154156551.9933850604434-0.23169028006339-0.39732012597993-0.227305020100621.38111984230290.127665770874741.0173046910646-0.076250378998353-0.124568054658461.56160339669480.331097459694610.95582258927268-104.5640121788317.936291170629-32.951147370161
154.69730952363663.0248363877916-4.83487914216262.2507776121607-3.2333252449024.9388352878536-0.12842346127073-0.91278414474334-1.9583283166225-0.524575467623910.35305040438904-0.179369977844681.0216292654947-0.696296819566230.086330098557280.69143299089138-0.0566531999568050.215020148529691.03647328559670.11592413657511.1540561810264-106.8860048259814.839035595788-42.291102792849
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 2 through 129)AA2 - 1291 - 128
22chain 'A' and (resid 130 through 336)AA130 - 336129 - 335
33chain 'A' and (resid 337 through 765)AA337 - 765336 - 449
44chain 'A' and (resid 766 through 917)AA766 - 917450 - 601
55chain 'A' and (resid 918 through 1044)AA918 - 1044602 - 721
66chain 'A' and (resid 1045 through 1140)AA1045 - 1140722 - 807
77chain 'B' and (resid 71 through 114)BC71 - 1142 - 45
88chain 'B' and (resid 115 through 184)BC115 - 18446 - 115
99chain 'B' and (resid 185 through 231)BC185 - 231116 - 153
1010chain 'B' and (resid 232 through 329)BC232 - 329154 - 251
1111chain 'B' and (resid 330 through 442)BC330 - 442252 - 356
1212chain 'C' and (resid 2022 through 2039)CE2022 - 20391 - 18
1313chain 'C' and (resid 2040 through 2064)CE2040 - 206419 - 43
1414chain 'C' and (resid 2065 through 2090)CE2065 - 209044 - 69
1515chain 'C' and (resid 2091 through 2114)CE2091 - 211470 - 93

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