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- PDB-9fik: Structure of the FAB fragment of the Antibody NTF30037 in complex... -

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Basic information

Entry
Database: PDB / ID: 9fik
TitleStructure of the FAB fragment of the Antibody NTF30037 in complex with NTF3
Components
  • NTF30037 Heavy Chain
  • NTF30037 Light Chain
  • Neurotrophin-3
KeywordsIMMUNE SYSTEM / NTF3 / phage display / X ray crystallography / antibody
Function / homology
Function and homology information


NTF3 activates NTRK3 signaling / NTF3 activates NTRK2 (TRKB) signaling / Activated NTRK3 signals through PLCG1 / Signaling by NTRK3 (TRKC) / nerve growth factor receptor binding / nerve growth factor signaling pathway / nerve development / induction of positive chemotaxis / Activated NTRK3 signals through PI3K / chemoattractant activity ...NTF3 activates NTRK3 signaling / NTF3 activates NTRK2 (TRKB) signaling / Activated NTRK3 signals through PLCG1 / Signaling by NTRK3 (TRKC) / nerve growth factor receptor binding / nerve growth factor signaling pathway / nerve development / induction of positive chemotaxis / Activated NTRK3 signals through PI3K / chemoattractant activity / positive regulation of receptor internalization / Activated NTRK3 signals through RAS / cell surface receptor protein tyrosine kinase signaling pathway / neuron projection morphogenesis / growth factor activity / modulation of chemical synaptic transmission / Constitutive Signaling by Aberrant PI3K in Cancer / synaptic vesicle / nervous system development / cell-cell signaling / PIP3 activates AKT signaling / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / regulation of apoptotic process / negative regulation of neuron apoptotic process / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of MAPK cascade / positive regulation of cell migration / axon / signaling receptor binding / positive regulation of cell population proliferation / dendrite / signal transduction / extracellular space / extracellular region
Similarity search - Function
Neurotrophin-3 / Neutrophin-3, N-terminal / Neutrophin-3 N-terminus / Nerve growth factor-related / Nerve growth factor conserved site / Nerve growth factor-like / Nerve growth factor family / Nerve growth factor family signature. / Nerve growth factor family profile. / Nerve growth factor (NGF or beta-NGF) / Cystine-knot cytokine
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Neurotrophin-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsGallego, P. / Aagaard, A. / Sjogren, T. / Chin, S. / Neal, F.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Slas Discov / Year: 2025
Title: Identification of unique binding mode anti-NTF3 antibodies from a novel long VH CDR3 phage display library.
Authors: Chin, S.E. / Gallego, P. / Aagaard, A. / Carmen, S. / Barrett, N. / Wolny, M. / Cloarec, S. / Paterson, J. / Sivapalan, R. / Hunt, J. / Murray, T.V. / Delaney, T. / Sjogren, T. / Neal, F.
History
DepositionMay 29, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 2, 2025Provider: repository / Type: Initial release
Revision 1.1Apr 9, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Neurotrophin-3
B: NTF30037 Heavy Chain
C: NTF30037 Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,38011
Polymers61,6853
Non-polymers6968
Water8,593477
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6250 Å2
ΔGint-30 kcal/mol
Surface area26530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.746, 108.549, 208.217
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Neurotrophin-3 / NT-3 / HDNF / Nerve growth factor 2 / NGF-2 / Neurotrophic factor


Mass: 13778.517 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NTF3 / Production host: Escherichia coli (E. coli) / References: UniProt: P20783

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Antibody , 2 types, 2 molecules BC

#2: Antibody NTF30037 Heavy Chain


Mass: 25181.148 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#3: Antibody NTF30037 Light Chain


Mass: 22725.016 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)

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Non-polymers , 4 types, 485 molecules

#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 477 / 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: 3.19 Å3/Da / Density % sol: 61.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5
Details: 15 % w/v Polyethylene glycol 8,000, 0.2 M Sodium Acetate, 0.1 M MES pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.8856 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Jan 19, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 1.859→58.68 Å / Num. obs: 51862 / % possible obs: 92.2 % / Redundancy: 13.4 % / Biso Wilson estimate: 21.18 Å2 / CC1/2: 0.996 / Net I/σ(I): 9.3
Reflection shellResolution: 1.859→2.032 Å / Num. unique obs: 2593 / CC1/2: 0.618

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
STARANISOdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.86→58.68 Å / SU ML: 0.1551 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.0879
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1862 --
Rwork0.1862 0 -
obs0.1862 51851 77.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.93 Å2
Refinement stepCycle: LAST / Resolution: 1.86→58.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4128 0 44 477 4649
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00784333
X-RAY DIFFRACTIONf_angle_d0.99655904
X-RAY DIFFRACTIONf_chiral_restr0.066659
X-RAY DIFFRACTIONf_plane_restr0.0079754
X-RAY DIFFRACTIONf_dihedral_angle_d6.9669618
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.86-1.880.316150.31615X-RAY DIFFRACTION
1.88-1.90.2989530.298953X-RAY DIFFRACTION
1.9-1.930.30721430.3072143X-RAY DIFFRACTION
1.93-1.950.29522540.2952254X-RAY DIFFRACTION
1.95-1.980.31274040.3127404X-RAY DIFFRACTION
1.98-20.2756540.275654X-RAY DIFFRACTION29.61
2-2.030.262510160.26251016X-RAY DIFFRACTION46.14
2.03-2.060.268814190.26881419X-RAY DIFFRACTION64.74
2.06-2.090.25817010.2581701X-RAY DIFFRACTION76.73
2.09-2.130.251219760.25121976X-RAY DIFFRACTION90.43
2.13-2.160.24710.24712139X-RAY DIFFRACTION96.79
2.16-2.20.24720.24722166X-RAY DIFFRACTION98.23
2.2-2.250.24050.24052181X-RAY DIFFRACTION98.24
2.25-2.290.23650.23652186X-RAY DIFFRACTION98.56
2.29-2.340.23480.23482155X-RAY DIFFRACTION98.4
2.34-2.40.234222120.23422212X-RAY DIFFRACTION98.57
2.4-2.460.225821630.22582163X-RAY DIFFRACTION98.45
2.46-2.520.217421750.21742175X-RAY DIFFRACTION98.42
2.52-2.60.210522170.21052217X-RAY DIFFRACTION98.88
2.6-2.680.215822160.21582216X-RAY DIFFRACTION99.15
2.68-2.780.222921610.22292161X-RAY DIFFRACTION98.54
2.78-2.890.195722010.19572201X-RAY DIFFRACTION98.92
2.89-3.020.19322230.1932223X-RAY DIFFRACTION98.89
3.02-3.180.181422170.18142217X-RAY DIFFRACTION99.46
3.18-3.380.169822320.16982232X-RAY DIFFRACTION99.11
3.38-3.640.151122140.15112214X-RAY DIFFRACTION99.1
3.64-40.138622490.13862249X-RAY DIFFRACTION99.51
4-4.580.120322510.12032251X-RAY DIFFRACTION99.12
4.58-5.770.129722810.12972281X-RAY DIFFRACTION99.65
5.78-58.680.174323770.17432377X-RAY DIFFRACTION98.96
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)
11.127243862410.475737935957-0.2145340496024.26725714090.614409533651.62042185843-0.06634898705020.276551589435-0.079351041363-0.3892607116320.1737332665460.236532886261-0.00706274710025-0.110428838229-0.03334533429820.2131674547980.0104957295268-0.03265140112150.08275553224060.01935011604040.228698819591-41.3791258811-50.6014164333-7.86944012161
20.164461698444-0.609481001633-0.1061361790632.416538923970.05497340895630.7674610667340.1920088989620.069733628722-0.534518888588-0.04558600420830.114490811142-1.271832729880.6560382801320.512859119228-0.2992848551930.3956962075460.09661667142090.04373072324960.0964039881743-0.1760710622090.999875253298-23.4681413098-56.1686913375-7.00308352548
35.73134127005-0.867245458544-0.4414724228953.67590769932-0.1637917380432.743537755650.1055766174760.496399296088-0.00351977221781-0.5111111622080.05762598168770.8249493440090.11684856246-0.509637933152-0.006277426040130.267651122992-0.0252344092447-0.07958301088710.1943715388870.02954241317080.417708169895-49.2902493598-55.3009338683-9.70568740233
40.450279411362-0.532117674799-0.7737780800942.92799070977-0.1301270135251.93260728690.3211058496730.252700014363-0.228168568611-0.07196398089420.04918424443670.432155136894-0.150599142058-0.420556528990.2409832258960.2397551713970.00492171761164-0.006550704388980.01298645274930.007638541495270.363682248499-48.5847574903-47.8628487905-4.0128067232
52.96528557143-0.4068590786272.336956381710.496307610252-0.1466179573753.75456242815-0.0575874647013-0.9459882158690.468198214860.33898153272-0.0557848431438-0.185078539545-0.4354868333840.1783920799820.4166198526850.24674267272-0.04647954246180.04401226132630.650884993952-0.1923375103550.253387213232-27.2920125079-20.111636931432.3433879599
63.07885937071-0.1566566429441.388257182340.499810218856-0.04250352262392.366605682090.163406814082-0.8590040485810.2359439866030.109559945181-0.106172321280.117494871611-0.0829092392602-0.3088032954430.03338475441080.192733027283-0.05722984318680.03507652066650.371830527247-0.04013781784330.179746857011-35.1123071663-25.130813210123.8610048202
73.18980354082-0.3064825474221.110838948511.14123353803-0.07842197082862.612228331250.146429836344-1.34032711760.1569249933670.127242537952-0.02504373426160.108395981524-0.123877465706-0.3649362643010.06485201829490.241195664955-0.07806198184970.0647083407680.693105429368-0.06398896201650.274949882828-37.1524475778-25.148463953630.6701856936
81.6665598850.1869490828680.8777960572950.0978693306783-0.09268121182942.429091061460.249358513542-1.00070460505-0.1595743086920.1643420882030.00792546086620.0995754311710.162536684925-0.0655292358446-0.1978418587080.2470745669-0.06193268091940.01361748667590.5404118206770.01360406781460.162039692296-27.4197263502-28.329094399330.0125658896
92.237466185650.1980048108691.287525082530.5531179041890.4293999085382.153639324520.0677591376278-0.7097189883660.0253488757440.0612643199241-0.0613102062090.0647292345561-0.0483156896712-0.119935531954-0.1257245236110.174579398471-0.03126156957070.03221405934190.308255180205-0.03749605933570.12876869037-29.7741544338-27.251409767421.3220847214
100.461929204857-0.4891609280160.8170952224822.3010959849-0.02401984472091.84422067261-0.1575198091190.1497747700250.0234235092441-0.2381307556620.11632077726-0.407755239089-0.1814001172431.108981734070.184334591210.32670500775-0.0838290178884-0.04810738152661.209425809490.02653531267230.2870381543359.81089631411-22.106124574540.2300495499
112.46021564705-0.227255050835-0.0710229516280.917731580996-0.642285870553.18911697359-0.147831193131-0.3449846613440.3006803278640.00255343790033-0.0320137036395-0.0343326416272-0.8176402676220.3271659753340.309040948590.480118050714-0.0221739736855-0.1110753035151.06558124867-0.04883271956490.262170550444-3.23865357806-17.346874694241.6206473454
123.33077550061-0.6004411162311.722177958151.249483793930.3196521853632.748227683290.122343498458-0.2409349946140.2901594562940.0911265685417-0.318328350249-0.248693214865-0.7067262081040.4244669573320.1254145608980.389143251796-0.0940918997915-0.06973224231940.8985741120590.006172488214430.2253090333763.02802887565-20.258537049636.2593757961
137.419635272150.9260490036332.069836650451.30926877488-0.008148537990682.53120927764-0.282700513883-0.3906157383750.7955152598930.2330269385370.0667316214567-0.341159805977-0.8961381803970.8642822490510.3887835559410.765192969182-0.263282967136-0.1239479500371.06235006271-0.01014755270030.4050505152718.52889378502-12.944220878144.1962947339
145.35585855756-2.786464086161.937979376491.76054094938-1.264242703290.9094773463350.0976811484909-0.003745604359760.3957527874680.02750647342930.0501234506152-0.274710401961-0.435266288380.490974131480.410380731890.515823683720.0132555954281-0.06525302318751.31726269021-0.07864299692190.3888884785154.07774378774-17.290959067348.0628205689
152.54247247270.7136535832030.2870441466241.356444172740.2105972606611.30574367809-0.0869137785407-0.217478206311-0.4781255910670.03913936811660.0857047153725-0.1067979962660.240070001517-0.05337900624750.04465640244540.206535502996-0.006491173996640.001065740413910.08808930563670.0362919993550.207903248142-14.1987462477-34.03990272548.6292463507
163.136025283820.1996734687210.3360367364960.3424893923350.2596539093681.80350832670.0780305174629-0.4928569981490.1558273088860.0736845173793-0.1482247457470.1506932076250.0210008360687-0.04621001587580.02927625324340.161505282986-0.03203040392610.01331929168560.0919092627335-0.003309675015210.135567994795-24.528588889-29.39509503911.9220628363
172.706645618320.6544507132090.4321807491520.9874522276080.4591744202882.06810198588-0.01526561692350.3293595337970.16155373166-0.267587685249-0.00812547431865-0.073729568875-0.193853031190.03353369154660.1694419092890.214904546511-0.02195186317660.01983954483840.0791421561304-0.006612167332140.236831904105-24.1601970245-26.4045480022.03247871228
182.330705006-0.102427546440.525716477850.1170565803060.3297188883311.9005137148-0.0183646539511-0.07301467599880.08238232445570.0820372498527-0.06377831720690.03138821608-0.1298804027960.03291019420980.1090747572450.177787602958-0.02574029332010.00613017685210.0720942662938-0.01488202348980.175791375913-13.7358912648-26.05264522324.56158429146
193.368675712790.6655760779760.659982270311.042490459980.7815750558751.271704681240.00369034366112-0.564846909786-0.368137784550.0879527506831-0.1448642842880.0303695821360.299605976999-0.07454967952690.06494064642140.207273008255-0.06747742760570.01777676297630.1417843839850.007120142361180.190600541406-27.3163387456-35.148028048915.6561259037
203.286544429110.3023136239160.825677848350.5074383572740.5018780974621.75758826650.044130568403-0.5413569225820.1313958182080.0274460340527-0.101848695452-0.01095846503030.1253157312630.3243675091250.007120322022640.173102479868-0.007499122225220.01112818633790.1555310918520.02797320451160.147959799747-1.21540711311-25.98883483612.8919102326
210.412139506716-0.1568852383361.031177354810.0425522058268-0.3521591923762.51183780234-0.0606827698512-0.770415491725-0.07220060496690.1104729661460.0108301567617-0.1397698197580.528226245240.57421236427-0.1927176234190.3314860617190.11628258343-0.03710020915340.8401690050360.106721125720.1896364298516.62949320675-30.685588315735.0289379887
221.58897467278-0.5370255999570.4734870146120.964996090789-0.1456085118680.141646158843-0.00331950759325-1.05791990991-0.9878592155710.2590394596110.04751234910890.03746490702290.8284894116420.429603736638-0.1471052976990.7934597837660.132962402893-0.01832954304050.8527763494640.2198450492080.4285067342694.23064263076-41.674002291533.853273949
234.684599318780.349347514395-0.04957424050822.98678565636-0.1013890608923.996693693560.170512171185-0.5416095597780.4308878353150.0844850865165-0.05334497673210.12664869778-0.3544910744480.0949373435328-0.0147996914380.211980694195-0.0139308845127-0.01796601397440.358971536497-0.03600515398950.214595669555-1.17783815871-21.297225731322.5929240214
241.03061053983-0.1410776737291.04918872530.15529119423-0.1342387075241.33911792351-0.0912533100611-0.805678354126-0.4741583953490.326593134748-0.0883867315413-0.3084967635320.8403459084190.510319759166-0.1972844061920.6536916271780.25770462309-0.003109974696241.052332671660.2811650001570.3176874807497.22488453078-37.188161273941.3644694441
252.59632088439-0.689630187374.104908384671.95001940449-2.537704060227.676157709970.0406860166294-0.763799443087-0.6304199024590.3537788993970.123273016254-0.1669772542070.7464790597390.785628549672-0.1998996918510.5871744456850.343803167554-0.0008675872848890.9020320171560.1771198994220.32223147233911.2070137086-37.867827378630.9114710215
261.628376320860.2130689796863.387651827580.1916261956360.2859836299537.197752932120.107481190728-0.656397967135-0.2153457799280.1482928315740.0794542471952-0.2463870784790.4433635297920.594296105216-0.1387978375970.4144037283960.244991908303-0.02271229394480.9072204845830.08285736086740.25060928630612.4494959741-34.28623232427.0371372488
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 11 through 36 )AA11 - 361 - 26
22chain 'A' and (resid 37 through 51 )AA37 - 5127 - 41
33chain 'A' and (resid 52 through 62 )AA52 - 6242 - 52
44chain 'A' and (resid 63 through 115 )AA63 - 11553 - 105
55chain 'B' and (resid -1 through 15 )BE-1 - 151 - 17
66chain 'B' and (resid 16 through 60 )BE16 - 6018 - 62
77chain 'B' and (resid 61 through 83 )BE61 - 8363 - 85
88chain 'B' and (resid 84 through 100 )BE84 - 10086 - 102
99chain 'B' and (resid 101 through 136 )BE101 - 136103 - 138
1010chain 'B' and (resid 137 through 160 )BE137 - 160139 - 158
1111chain 'B' and (resid 161 through 174 )BE161 - 174159 - 172
1212chain 'B' and (resid 175 through 205 )BE175 - 205173 - 203
1313chain 'B' and (resid 206 through 217 )BE206 - 217204 - 215
1414chain 'B' and (resid 218 through 232 )BE218 - 232216 - 230
1515chain 'C' and (resid 3 through 25 )CG3 - 251 - 23
1616chain 'C' and (resid 26 through 49 )CG26 - 4924 - 47
1717chain 'C' and (resid 50 through 70 )CG50 - 7048 - 68
1818chain 'C' and (resid 71 through 84 )CG71 - 8469 - 82
1919chain 'C' and (resid 85 through 104 )CG85 - 10483 - 102
2020chain 'C' and (resid 105 through 117 )CG105 - 117103 - 115
2121chain 'C' and (resid 118 through 154 )CG118 - 154116 - 152
2222chain 'C' and (resid 155 through 165 )CG155 - 165153 - 163
2323chain 'C' and (resid 166 through 177 )CG166 - 177164 - 175
2424chain 'C' and (resid 178 through 191 )CG178 - 191176 - 189
2525chain 'C' and (resid 192 through 201 )CG192 - 201190 - 199
2626chain 'C' and (resid 202 through 212 )CG202 - 212200 - 210

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