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- PDB-13ha: The structure of Fab_C1 in complex with CD30 -

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Basic information

Entry
Database: PDB / ID: 13ha
TitleThe structure of Fab_C1 in complex with CD30
Components
  • FabS1CE2_C1 heavy chain
  • FabS1CE2_C1 light chain (Trastuzumab Fab Light Chain)
  • Tumor necrosis factor receptor superfamily member 8
KeywordsIMMUNE SYSTEM / high-affinity binding / immune suppression / tumour growth suppressor / cell signalling / cytokine receptor
Function / homology
Function and homology information


positive regulation of TRAIL production / TNFs bind their physiological receptors / cellular response to mechanical stimulus / positive regulation of tumor necrosis factor production / transmembrane signaling receptor activity / protease binding / positive regulation of apoptotic process / negative regulation of cell population proliferation / signal transduction / extracellular exosome ...positive regulation of TRAIL production / TNFs bind their physiological receptors / cellular response to mechanical stimulus / positive regulation of tumor necrosis factor production / transmembrane signaling receptor activity / protease binding / positive regulation of apoptotic process / negative regulation of cell population proliferation / signal transduction / extracellular exosome / plasma membrane / cytoplasm
Similarity search - Function
Tumour necrosis factor receptor 8 / Tumour necrosis factor receptor 8, N-terminal / : / TNFR/NGFR family cysteine-rich region domain profile. / TNFR/NGFR cysteine-rich region / TNFR/NGFR family cysteine-rich region signature. / Tumor necrosis factor receptor / nerve growth factor receptor repeats. / TNFR/NGFR cysteine-rich region
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Tumor necrosis factor receptor superfamily member 8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMallette, E. / Singer, A.U. / Blazer, L.L. / Adams, J.J. / Suits, M.D.L. / Sidhu, S.S.
Funding support Canada, 2items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)MOP-93725 Canada
Canadian Institutes of Health Research (CIHR)MOP-136944 Canada
CitationJournal: Protein Sci. / Year: 2026
Title: Strategy for modular assembly of tetravalent, multispecific antibodies.
Authors: Mallette, E. / Blazer, L.L. / Hokanson, C.A. / Chen, C. / Perez, J.G. / Pavlenco, A. / Ploder, L. / Singer, A.U. / Suits, M.D.L. / Bhakta, S. / Junutula, J.R. / Adams, J.J. / Sidhu, S.S.
History
DepositionMay 5, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: FabS1CE2_C1 heavy chain
C: FabS1CE2_C1 light chain (Trastuzumab Fab Light Chain)
A: Tumor necrosis factor receptor superfamily member 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,81025
Polymers58,7043
Non-polymers1,10622
Water9,656536
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8950 Å2
ΔGint-110 kcal/mol
Surface area23730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.150, 72.150, 220.042
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

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Components

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Protein , 1 types, 1 molecules A

#3: Protein Tumor necrosis factor receptor superfamily member 8 / CD30L receptor / Ki-1 antigen / Lymphocyte activation antigen CD30


Mass: 11263.815 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNFRSF8, CD30, D1S166E / Plasmid: PSDCSTA
Details (production host): C-terminal 6-His tag with thrombin cleavage site N-terminal to 6His
Cell line (production host): Expi293 / Production host: Homo sapiens (human) / References: UniProt: P28908

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Antibody , 2 types, 2 molecules BC

#1: Antibody FabS1CE2_C1 heavy chain


Mass: 24214.174 Da / Num. of mol.: 1 / Mutation: K123Q and E154G
Source method: isolated from a genetically manipulated source
Details: FAB PRODUCED BY RANDOMIZATION OF CDR REGIONS AND SELECTED BY PHAGE DISPLAY.
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PSDCSTA / Cell line (production host): Expi293 / Production host: Homo sapiens (human)
#2: Antibody FabS1CE2_C1 light chain (Trastuzumab Fab Light Chain)


Mass: 23225.684 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: FAB PRODUCED BY RANDOMIZATION OF CDR REGIONS AND SELECTED BY PHAGE DISPLAY.
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PSDCSTA / Cell line (production host): Expi293 / Production host: Homo sapiens (human)

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Non-polymers , 5 types, 558 molecules

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


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 536 / 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: 2.83 Å3/Da / Density % sol: 56.53 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 20% PEG3350 and 0.1M Bis-tris methane, pH 5.5. Cryoprotected with the same buffer plus 30% ethylene glycol
Temp details: room temperature

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.919907 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 10, 2026 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.919907 Å / Relative weight: 1
ReflectionResolution: 2→220.04 Å / Num. obs: 46203 / % possible obs: 100 % / Redundancy: 20 % / Biso Wilson estimate: 11.7 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.165 / Rpim(I) all: 0.053 / Rrim(I) all: 0.174 / Net I/σ(I): 12
Reflection shellResolution: 2→2.03 Å / Redundancy: 18.6 % / Rmerge(I) obs: 2.421 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 2246 / CC1/2: 0.394 / Rpim(I) all: 0.808 / Rrim(I) all: 2.557 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
autoPROCdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→47.56 Å / SU ML: 0.2196 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.7877
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2223 2366 5.14 %
Rwork0.1892 43650 -
obs0.1909 46016 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44 Å2
Refinement stepCycle: LAST / Resolution: 2→47.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3904 0 61 536 4501
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00784049
X-RAY DIFFRACTIONf_angle_d0.93475491
X-RAY DIFFRACTIONf_chiral_restr0.0591620
X-RAY DIFFRACTIONf_plane_restr0.0077704
X-RAY DIFFRACTIONf_dihedral_angle_d15.0591436
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.040.35391270.31012445X-RAY DIFFRACTION96.66
2.04-2.080.2911560.2752514X-RAY DIFFRACTION100
2.08-2.130.31871280.26432546X-RAY DIFFRACTION100
2.13-2.180.29611610.24462532X-RAY DIFFRACTION99.96
2.18-2.240.27681370.22632524X-RAY DIFFRACTION100
2.24-2.310.26141610.22432498X-RAY DIFFRACTION100
2.31-2.380.22471080.22062578X-RAY DIFFRACTION100
2.38-2.470.26341450.21272518X-RAY DIFFRACTION100
2.47-2.570.24621360.21182557X-RAY DIFFRACTION100
2.57-2.690.22221250.20112589X-RAY DIFFRACTION100
2.69-2.830.22741390.2022546X-RAY DIFFRACTION99.96
2.83-30.26061390.20182579X-RAY DIFFRACTION99.96
3-3.240.26491410.19142558X-RAY DIFFRACTION99.96
3.24-3.560.19511550.17022575X-RAY DIFFRACTION99.96
3.56-4.080.20411140.16712637X-RAY DIFFRACTION99.96
4.08-5.130.18921380.14632659X-RAY DIFFRACTION100
5.14-47.560.17591560.18772795X-RAY DIFFRACTION100
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)
11.974682971450.309528088865-0.7524739411821.671510381690.5175230888321.42585206354-0.5238174594050.3192504636160.593976548917-0.1247070709910.371235417937-0.00753130346704-0.3597160555040.05247361685980.006027685158180.517389635319-0.07623544546160.06082273630510.329955612007-0.05210822406830.399549163966-35.115993237849.905106002317.4342952676
23.30852476765-2.1730500239-1.185494858791.79650404620.1116247897251.09566004130.217725619575-0.09450881641270.843124499468-0.1861078504440.058407791004-0.0896421745157-0.6062777138730.105048892227-0.2045215548030.609657850996-0.0124673184644-0.03155194516870.35264019709-0.04595294979960.512789225274-44.749442167455.766173086722.7515254079
31.214734214560.432204573617-0.1287753315071.065178932270.1880975193912.29043789756-0.119632719768-0.31605457857-0.0285918229081-0.2987709144920.254178834249-0.106812912194-0.324040869940.248429200554-0.002681444299720.363874964142-0.07209144423590.01679169905410.387854781734-0.07180267748610.276072086341-41.16171362544.663757751127.701540714
41.963242217190.3553773321660.2085027635510.8307803399950.4138641392282.085672282970.0070953165433-0.3902997669520.3941402656370.0290448250576-0.05408329464490.226378099569-0.2611021134320.1137867601280.05896945675690.379340120751-0.05533391600890.0005653333222290.410751224124-0.09028674889920.394317226164-36.524369038652.107120502931.524206094
52.494964198-0.3051929789690.05353300065411.022363596021.136570715641.41307081047-0.0760209874512-0.3079700087760.2779965719230.1422890338880.1978731061330.0396773591408-0.2694862103160.231151742570.006027648730780.475787977033-0.1002323264330.08205343676560.40701378894-0.07071177051820.401905325085-31.38114193248.364369196724.7579593741
60.627482171328-0.150561093194-0.4743259817050.6318609303840.6879040396861.03407491430.07773268803670.03655721305290.142718093866-0.161375965699-0.04177374429020.0539458605151-0.251026998894-0.0889031711015-0.006740492965940.429316681114-0.05386348539980.01541413704690.338735962388-0.02650173201060.29935478385-40.305678833144.299081171820.5983260217
71.543321805531.09292400853-0.2477131076011.609465969710.06325702115160.8386308751850.0942433026572-0.0136949363196-0.00200353546472-0.0585203224519-0.03431133330690.03145519999370.0197205186447-0.00891252048715-0.009259267415870.369309515703-0.06054440246140.03618885547270.270677174876-0.02666502182020.2974472596-27.219935265325.2318048832-0.275372324137
81.839302407862.395556165412.247318438794.148545574063.720575181425.88169218041-0.232907792299-0.02857726757830.107173069307-0.6526728067330.1421130931120.345043583275-0.6208252577510.04707262236090.1776437351450.466798444179-0.0734276920159-0.003963296264070.267780964607-0.00186566012130.327908829851-26.41074208833.265094265-4.76047117382
91.909434418171.967248523441.186518845962.521552826741.661393993615.965171237910.004338740401230.182002020864-0.0845043849008-0.1725179641460.0555385281874-0.6485454980760.3878652692510.277558842423-0.09116985341470.452910954893-0.07013354535950.09416140108510.379065861850.002307069920820.361206804103-20.697457826128.8562984129-7.4857856076
101.399485641470.914371993140.6445228849492.050578664230.6165588339682.38993850950.0602850818463-0.232810718443-0.1275213669640.21758871125-0.07806044746690.1415669103170.324780945405-0.004385976417480.007468679414110.359571327208-0.03304077875970.01776653660860.3811113442790.009354394314630.314439463607-49.889163145724.164872569424.8450028901
111.613265008070.735697690169-0.0114117537452.301631149360.9651981109131.7128980132-0.0335900680936-0.1951883884810.0033521412190.087697425035-0.05915898075730.1317510132140.0339223625318-0.09062640128330.0308489110420.344074606145-0.0106538399632-0.007484826055240.3959847409-0.01558842816620.289830344641-55.356289045432.701570165626.5880026984
121.469957394620.696802220971-0.2106735753141.452536929140.8819952957462.0215021812-0.0282744557005-0.152982413355-0.02251461316280.0610693830525-0.05071907502010.062607333650.063924032683-0.2164976248360.01425537408350.359808137211-0.01344159826460.0358582707150.3460582780640.00661231256640.310418482452-50.722379575832.535752995723.8363218328
130.892460578402-1.63841157694-1.926482103182.119670289422.577907727072.688159421760.009099373441610.0900864779951-0.2740690480770.28744803745-0.06842572357590.01779651770710.227817389661-0.28310155277-0.06931672840740.392988361232-0.079353981540.0709328941690.357224195974-0.06227498526880.427862347561-45.933359132916.497398185211.1520811299
143.582753251041.24068028879-0.09758232171832.90779629312-0.3258942484291.37498299812-0.395873761267-0.008855738001920.786618588971-0.451620264419-0.0288876770268-0.0497985687155-0.1006327430030.218432627310.03326289133010.351389667963-0.080477189530.01039766778540.299799944075-0.00552450385480.368059153107-17.871612373318.7841376471-0.296804477634
153.953225780920.2698505738710.06588312753581.50762584218-0.1382685421641.11974125329-0.057380391488-0.2971235522230.05909769514570.1043824235970.0009837514554180.203790786731-0.0570542303736-0.0154867720427-0.02362755114780.353582190823-0.07668645557080.02068902025660.266054998347-0.03110754544190.361267443694-29.118028234413.56330290928.30483824717
162.94774560421-1.1151842165-0.4958792178841.53953779679-0.375642046130.310098836063-0.0165355301612-0.155003178029-0.1215511174260.355151777595-0.015328675849-0.1624061333320.1664312324370.16794722420.05434469747890.439927589546-0.122318850554-0.02057897672990.408055484025-0.0204216700480.366337942493-20.965736897412.747066877712.9583456898
177.342702316342.34863722523-0.3697565094275.435097582120.9225493070311.63972420032-0.6668605862690.1248043664840.887097970609-0.5445084778930.2963962334770.587635486954-0.629398303468-0.1983508320620.1282902337030.394114820389-0.0738398159635-0.002283744308850.358659583468-0.05683512575030.435697594071-42.433016023821.13309090436.01179724196
186.497424340710.382025218455-0.2003565268872.24698046839-0.02390776253811.709375000040.08055322547390.1162241349650.130591144730.00517678291333-0.153971299804-0.7431683991570.05386555435360.3034512616160.03283098809060.379563832333-0.0927109919649-0.01129560768410.3797025355740.01212689652750.432779539071-14.319108767815.95018565517.15255892901
195.326535777880.610217069921-0.2716660268642.60521514457-0.2197147248941.71340294319-0.03484822717650.205662826183-0.293668280505-0.0076229084853-0.0843195932079-0.4093924671050.1211197754630.08188704287410.03724062449310.410976124387-0.09165971386070.04748557589540.267297171697-0.003753610033960.425167323077-22.27908561996.406852745243.67061055708
203.69050979698-2.73743605687-2.610731237292.01520460346-0.6206479017814.31071743881-0.622150965515-0.09208891654220.5176302216530.9511639121130.253013097179-0.687919279869-0.6648830936861.022582681460.1437869729550.624658685706-0.0331299508601-0.1283784099960.562023480678-0.05026333993910.648631334541-41.000871239262.984245138861.0331910501
213.41468577034-0.655503511429-0.2781538214545.575275942820.1973089827270.0310280235728-0.0690122343226-0.682537676212-0.358423561471.27667953974-0.0284779616038-0.412667827041-0.4410379575370.6073446094530.2077705303960.5863108588710.0586591616003-0.1201033540320.873081899682-0.1378201192330.506715707105-39.485867268155.81036717864.4976154685
221.16937893207-1.149387407371.276329166752.2430554565-0.1867499408654.104195394340.119646094771-0.2419221031550.206479972242-0.354477120164-0.0414463847559-0.151426583445-0.5673679166730.711282378667-0.001942923037930.480887860643-0.04057390062320.09551842671640.506968367609-0.009513943090050.366622386221-50.399982258360.596045402448.0196330796
238.68873052686-0.5055180927150.01780077158976.87582149701-0.971759177380.195105235483-0.347207549772-1.807502352010.1811628630451.72810232225-0.28127288520.326233110253-0.7346553169830.01553650758520.04623346648720.6404788792140.01058047484170.003670730932440.685620286052-0.08722425190910.368466317293-48.642456350560.906422339661.3017068975
248.138304412250.9634957200074.881638988031.192970268790.8685977261953.036959765520.359970600774-0.1845751547930.2645204631230.302197631958-0.009826647989930.348018517917-0.4481090645-0.394945759453-0.01461640224370.449834746431-0.01325228165440.09301073215930.3954128814560.01856254340490.461724481672-55.907304320657.222719442545.5745070475
251.36654733323-0.6272764605660.1582628742981.466714613170.06165206965781.47892914460.06337963749690.0939651433894-0.326736606476-0.2073137149820.0797332904082-0.08483015176920.0305017972783-0.0179351767024-0.07443348024730.441112120202-0.008839596626040.01250798321410.467170005785-0.1072064661580.447246341794-55.990448052449.576750711238.8103759591
263.387984433730.07315532535470.5140816755913.317184689440.3597953856092.245443509540.334498680524-0.36540259659-0.5145812822230.218051479593-0.2450575973140.09292917300640.130752888545-0.5650699698410.09596067110750.397884250115-0.03076680210390.05937735787270.513568921092-0.04853305139490.555066949609-66.613367034244.398708658538.9246071034
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'B' and (resid 1 through 17 )BA1 - 171 - 17
22chain 'B' and (resid 18 through 32 )BA18 - 3218 - 32
33chain 'B' and (resid 33 through 55 )BA33 - 5533 - 55
44chain 'B' and (resid 56 through 76 )BA56 - 7656 - 76
55chain 'B' and (resid 77 through 91 )BA77 - 9177 - 91
66chain 'B' and (resid 92 through 125 )BA92 - 12592 - 125
77chain 'B' and (resid 126 through 196 )BA126 - 196126 - 196
88chain 'B' and (resid 197 through 209 )BA197 - 209197 - 209
99chain 'B' and (resid 210 through 222 )BA210 - 222210 - 222
1010chain 'C' and (resid 1 through 18 )CJ1 - 181 - 18
1111chain 'C' and (resid 19 through 75 )CJ19 - 7519 - 75
1212chain 'C' and (resid 76 through 101 )CJ76 - 10176 - 101
1313chain 'C' and (resid 102 through 113 )CJ102 - 113102 - 113
1414chain 'C' and (resid 114 through 128 )CJ114 - 128114 - 128
1515chain 'C' and (resid 129 through 150 )CJ129 - 150129 - 150
1616chain 'C' and (resid 151 through 163 )CJ151 - 163151 - 163
1717chain 'C' and (resid 164 through 174 )CJ164 - 174164 - 174
1818chain 'C' and (resid 175 through 188 )CJ175 - 188175 - 188
1919chain 'C' and (resid 189 through 212 )CJ189 - 212189 - 212
2020chain 'A' and (resid 69 through 75 )AZ69 - 751 - 7
2121chain 'A' and (resid 76 through 83 )AZ76 - 838 - 15
2222chain 'A' and (resid 84 through 96 )AZ84 - 9616 - 28
2323chain 'A' and (resid 97 through 104 )AZ97 - 10429 - 36
2424chain 'A' and (resid 105 through 111 )AZ105 - 11137 - 43
2525chain 'A' and (resid 112 through 135 )AZ112 - 13544 - 67
2626chain 'A' and (resid 136 through 152 )AZ136 - 15268 - 84

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