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- PDB-8bbo: SARS-CoV-2 Delta-RBD complexed with BA.2-36 Fab -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 8bbo
TitleSARS-CoV-2 Delta-RBD complexed with BA.2-36 Fab
Components
  • IGH@ protein
  • Immunoglobulin kappa light chain
  • Spike glycoprotein
KeywordsVIRAL PROTEIN / SARS-CoV-2 / BA.2 mAb / RBD / BA.2-36
Function / homology
Function and homology information


immunoglobulin complex / immunoglobulin complex, circulating / immunoglobulin receptor binding / complement activation, classical pathway / antigen binding / endocytosis involved in viral entry into host cell / antibacterial humoral response / adaptive immune response / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated virion attachment to host cell ...immunoglobulin complex / immunoglobulin complex, circulating / immunoglobulin receptor binding / complement activation, classical pathway / antigen binding / endocytosis involved in viral entry into host cell / antibacterial humoral response / adaptive immune response / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated virion attachment to host cell / blood microparticle / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / host cell plasma membrane / virion membrane / extracellular space / extracellular exosome / membrane / plasma membrane
Similarity search - Function
Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain ...Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, betacoronavirus / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2 / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Spike glycoprotein / Immunoglobulin kappa light chain / IGH@ protein
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsZhou, D. / Ren, J. / Stuart, D.I.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
CAMS Innovation Fund for Medical Sciences (CIFMS)2018-I2M-2-002 United Kingdom
Medical Research Council (MRC, United Kingdom)MR/N00065X/1 United Kingdom
CitationJournal: Cell Rep / Year: 2023
Title: Rapid escape of new SARS-CoV-2 Omicron variants from BA.2-directed antibody responses.
Authors: Aiste Dijokaite-Guraliuc / Raksha Das / Daming Zhou / Helen M Ginn / Chang Liu / Helen M E Duyvesteyn / Jiandong Huo / Rungtiwa Nutalai / Piyada Supasa / Muneeswaran Selvaraj / Thushan I de ...Authors: Aiste Dijokaite-Guraliuc / Raksha Das / Daming Zhou / Helen M Ginn / Chang Liu / Helen M E Duyvesteyn / Jiandong Huo / Rungtiwa Nutalai / Piyada Supasa / Muneeswaran Selvaraj / Thushan I de Silva / Megan Plowright / Thomas A H Newman / Hailey Hornsby / Alexander J Mentzer / Donal Skelly / Thomas G Ritter / Nigel Temperton / Paul Klenerman / Eleanor Barnes / Susanna J Dunachie / / Cornelius Roemer / Thomas P Peacock / Neil G Paterson / Mark A Williams / David R Hall / Elizabeth E Fry / Juthathip Mongkolsapaya / Jingshan Ren / David I Stuart / Gavin R Screaton /
Abstract: In November 2021, Omicron BA.1, containing a raft of new spike mutations, emerged and quickly spread globally. Intense selection pressure to escape the antibody response produced by vaccines or ...In November 2021, Omicron BA.1, containing a raft of new spike mutations, emerged and quickly spread globally. Intense selection pressure to escape the antibody response produced by vaccines or severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection then led to a rapid succession of Omicron sub-lineages with waves of BA.2 and then BA.4/5 infection. Recently, many variants have emerged such as BQ.1 and XBB, which carry up to 8 additional receptor-binding domain (RBD) amino acid substitutions compared with BA.2. We describe a panel of 25 potent monoclonal antibodies (mAbs) generated from vaccinees suffering BA.2 breakthrough infections. Epitope mapping shows potent mAb binding shifting to 3 clusters, 2 corresponding to early-pandemic binding hotspots. The RBD mutations in recent variants map close to these binding sites and knock out or severely knock down neutralization activity of all but 1 potent mAb. This recent mAb escape corresponds with large falls in neutralization titer of vaccine or BA.1, BA.2, or BA.4/5 immune serum.
History
DepositionOct 14, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 22, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 12, 2023Group: 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_PubMed / _citation.title / _citation_author.name
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
R: Spike glycoprotein
H: IGH@ protein
L: Immunoglobulin kappa light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,4464
Polymers70,2243
Non-polymers2211
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5940 Å2
ΔGint-19 kcal/mol
Surface area27430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.141, 99.141, 86.054
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41
Space group name HallP4w
Symmetry operation#1: x,y,z
#2: -y,x,z+1/4
#3: y,-x,z+3/4
#4: -x,-y,z+1/2

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Components

#1: Protein Spike glycoprotein / S glycoprotein / E2 / Peplomer protein


Mass: 22935.734 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Production host: Homo sapiens (human) / References: UniProt: A0A8B6RM54
#2: Antibody IGH@ protein


Mass: 23849.586 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGH@ / Production host: Homo sapiens (human) / References: UniProt: Q6GMX6
#3: Antibody Immunoglobulin kappa light chain / Immunoglobulin kappa light chain EU


Mass: 23439.061 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) / References: UniProt: P0DOX7
#4: 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: obtained synthetically / 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
Has ligand of interestN

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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: 3.01 Å3/Da / Density % sol: 59.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 2% (v/v) PEG400, 0.1M imidazole pH7.0 and 24% (w/v) PEG MME 5000.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97628 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Oct 5, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97628 Å / Relative weight: 1
ReflectionResolution: 2.75→55 Å / Num. obs: 21850 / % possible obs: 100 % / Redundancy: 26.8 % / Biso Wilson estimate: 64.52 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.46 / Rpim(I) all: 0.09 / Net I/σ(I): 7.5
Reflection shellResolution: 2.75→2.8 Å / Mean I/σ(I) obs: 0.4 / Num. unique obs: 1103 / CC1/2: 0.39

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Processing

Software
NameVersionClassification
GDA1.20.1_4487data collection
PHENIX1.20.1_4487refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7PS6

7ps6


Resolution: 2.75→49.57 Å / SU ML: 0.4107 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.6982
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.252 1102 5.06 %
Rwork0.2242 20668 -
obs0.2256 21770 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 80.7 Å2
Refinement stepCycle: LAST / Resolution: 2.75→49.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4738 0 14 0 4752
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00184868
X-RAY DIFFRACTIONf_angle_d0.46746622
X-RAY DIFFRACTIONf_chiral_restr0.0425736
X-RAY DIFFRACTIONf_plane_restr0.004850
X-RAY DIFFRACTIONf_dihedral_angle_d10.34971739
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.75-2.870.31161130.33792538X-RAY DIFFRACTION98.08
2.87-3.030.35571530.30152542X-RAY DIFFRACTION100
3.03-3.210.34381200.29722612X-RAY DIFFRACTION99.96
3.22-3.460.33141170.27472599X-RAY DIFFRACTION99.96
3.46-3.810.29221660.24862554X-RAY DIFFRACTION100
3.81-4.360.23011280.20562600X-RAY DIFFRACTION100
4.36-5.50.19661610.17692581X-RAY DIFFRACTION100
5.5-49.570.21631440.18322642X-RAY DIFFRACTION99.86
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)
13.39998855016-0.03778093574732.09826530840.1331086499290.1462619576731.924354954220.643779088774-0.008366661714580.930991121137-0.889967706008-0.355549476935-0.171442574439-1.607180365261.10024791202-0.1799430810111.25521358064-0.3341009394860.3094327993540.929836758925-0.2305577817230.765018806655-33.36509842713.273462984821.30879266791
25.08577836764-2.22839059616-2.036590646145.803304541615.340890780564.881164905350.56779292425-0.5009493639371.67844384927-0.109086120441-0.4392173861390.145010636865-2.414431270510.267321936216-1.530577984831.65960712548-0.6456637257210.9679253659761.09607940533-0.137943102520.281661311033-29.285135361611.0522676453-5.63561616447
37.31064673625-1.12424841323-4.2318503963.62951165616-1.443092737756.380142579540.810543676923-0.5590345524231.321484852120.4835577813670.548062767004-0.743727888349-1.28634264226-0.0860368662211-0.4148693021971.34344848206-0.7393078253030.1115584196431.26984412343-0.6098305910870.667113067575-26.432510224713.280164667610.2621690989
4-0.01195104338920.0338669919928-0.014839300550.00402458241832-0.008596765664570.021013061782-0.212751405590.3275048319991.55532044826-0.447567097053-0.320461969995-0.726085798888-1.23222470379-0.207239691590.02974155779011.96971109605-0.3818185031370.3604789004661.223128493690.05524655553521.65802358658-20.110417999118.76337911970.252222464716
52.17730972308-0.775205389851-1.548704519292.400177623650.8308401892652.910097370580.210564305156-0.6471311878040.27124784577-0.146345171560.0542496415773-0.682360165821-0.6563352991491.43549704301-0.2709520173230.594659897632-0.2275018670060.04872322778061.2486942793-0.2393449363150.647989415452-24.0538008279-4.534754705736.26883007698
60.1445001372330.54064753192-0.03957583230043.96009559182-0.08642031641220.0544359612597-0.247947073030.0277182932682-0.535376344216-0.781353691669-0.406017053107-1.47406133290.2911305818580.1087567366440.01764294355180.7957215244810.1362712389950.06066876652351.386649602980.07533606821691.07203526245-20.5785316853-26.7726487977-0.0589722745294
72.193250419172.672173313671.261361870363.409496917462.55495459246.612134913010.512603051547-1.0289527805-0.7885521891551.73207017801-0.578459376147-1.907125421841.974708184210.7833700250150.7503110206730.8757025833660.190896716756-0.08862536019641.208627965260.2640545543081.05861066146-25.5723844752-25.68866937483.74281385817
81.8356162731-0.644309318163-0.0220413844152.254933535062.075651075392.489226177990.266252275641-0.794446112919-0.0340852790763-0.146470892319-0.0738951350957-0.587908032088-0.3437895671471.62157011968-0.04044995780180.553878022031-0.151897617371-0.05325285875721.16059813025-0.3202921880570.744466511422-30.2591130218-2.2960262235313.1795691615
93.530478661840.227277003929-0.6609974739062.45142744192-0.08811152761964.179093335750.3546490641070.52319228044-0.440524324398-0.426326540054-0.1925199707270.3678937663750.6383841140110.211989284024-0.09313122808540.6349062348570.131365166550.03558113587280.5670131692420.07457821597310.604785621935-54.5663180919-31.9950554186-0.0206584039304
102.71096802951.344799597250.1090439239144.451300731630.4480415510293.33289422034-0.18465764572-0.191531870629-0.138199048932-0.06666281058850.203844593048-0.02446255859590.008456004115190.351330704177-0.04490521150690.3587019397580.07269722604820.03548267147350.4107976467050.03815023455730.370487335638-47.7626577623-24.8377847434.27879040546
114.287318106011.2262863480.8168002995063.276574938581.100153847552.5079467624-0.3514227681850.03692390222690.00744556572414-0.4580129089880.2292077310950.302100493972-0.04302745220430.08302737631340.05450194025170.3992765923680.06133810922190.07098916418610.4045675253870.03159485222250.352364150171-56.7538131677-25.22744987950.237160716745
120.8384421855031.11006409525-0.6956389154384.1074166994-0.02935006976630.916172427396-0.137753875382-0.3639445518951.16123142056-0.3350315518960.00540550178763-1.123882193530.0173630179937-0.321633709359-0.01288987276360.3841946349720.0659008119013-0.07652845990880.5969250751040.02408100557540.654252740315-92.4246616549-27.3787719768-8.74340664941
134.366339034681.119115280360.09690024968581.39220966638-0.372906184331.328149746760.01114895412310.109505926109-0.7809189967650.103959459522-0.116921895937-0.255738026577-0.06095590038320.4178774788150.1510402546030.3108275101040.0464009426430.03793421202540.4137293057940.08463913977040.532075507834-80.2935230215-29.3705524686-9.604002812
146.76907440578-0.63530655397-1.799586197920.4044626069080.1837352472191.4232741459-0.6553064426110.91985257045-1.566223084510.19058267544-0.0317160241315-0.1422755367480.525782593719-0.007347990601830.1794327553860.6153463570720.01768245891690.04131122173540.579976735281-0.07533749800840.773413035458-86.7371033318-36.1965563994-12.4982191996
153.40458260831-1.192480579460.6672662301941.08915156604-0.1280971912171.948029350250.0843722404749-0.1372363712270.2205719507690.2322750195410.4694241825780.596046186903-0.8457167548150.0241908321287-0.3514770691110.666466739975-0.01134461858110.1018665579070.3868054059260.002837279531350.599708360843-64.8247677519-2.504724342962.45122943776
163.8289252247-0.4805588900390.6717246698983.22412865929-0.4757851896173.003982864980.192710446091-0.1100361143950.400977501775-0.02072766570050.07495071487350.0228248107682-0.4153132526970.342344302891-0.1975669132280.392024981826-0.08525181096790.1170670711140.32870959652-0.03135093837930.367542310607-54.0773959048-5.01546141871-0.178647009006
173.61863281854-1.325682276711.814555310682.062942263370.5245392656873.33607226011-0.155558824456-0.1641818648480.2114686343570.0601284524340.2428008184330.121324363711-0.3016907220670.118296885203-0.2405606177520.51644050036-0.02875277892530.141664917640.418040654694-0.01249500802270.434227689785-57.1861132858-4.564466660011.53709240885
181.410744645120.02702383000010.4953420860140.06887669052260.1094059440320.29293767340.3621239752880.5732974934740.560412327358-0.393240696828-0.03421126321280.504215564273-0.715354671421-0.257951106785-0.3929437829370.6859127726460.0737434045119-0.01417608263140.5795757584840.1699584310050.713113305253-78.5144416171-5.10794450329-6.41888233431
192.802578971870.384859510966-0.6339699555123.70823430985-0.9055815279732.21989159229-0.409748739264-0.0714939467077-0.633198526388-0.1842766795780.458419823564-0.507385909125-0.124682271392-0.566386472963-0.1379404802680.4814410800950.02777605790460.02541213782680.5479973860640.1634075805780.609030376229-88.3103033106-24.5336414122-2.36882795362
203.22218377081.42119551621-2.35998530391.47974417957-2.155448094453.02610198439-0.137927689535-0.985594933448-0.2287610480261.189561814420.02239392416140.31319221431-1.20538819334-1.23354661549-0.2814484269580.6475250593130.1590480536560.1130024587890.9049188712420.1451208249270.6630071151-93.441801941-19.85581977529.08353810909
213.570531645210.04205607079181.253130044923.07093167023-1.759624653292.764993138880.4349323759990.006866236348290.0477669516190.363337438016-0.1088952156880.481652381977-0.849809124426-0.1285139645020.1685214488620.6661691398470.157804446694-0.01326246899890.5281680182950.06303448242820.518099920926-79.3647774703-16.2998799498-3.33634046977
222.711446470320.166196312894-0.217705573152.87624331093-1.522023368622.86672067450.0979462929994-0.419520632652-0.08696494617830.6823108949060.2815553264220.901232507184-0.311227793601-0.519822074436-0.2888159583310.4593502722730.1284619771520.08047848613630.7331991161870.1654406221840.721941288382-94.3981042091-23.09185897763.89969248522
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'R' and (resid 335 through 353 )RA335 - 3531 - 19
22chain 'R' and (resid 354 through 364 )RA354 - 36420 - 30
33chain 'R' and (resid 365 through 380 )RA365 - 38031 - 46
44chain 'R' and (resid 381 through 394 )RA381 - 39447 - 60
55chain 'R' and (resid 395 through 469 )RA395 - 46961 - 135
66chain 'R' and (resid 470 through 479 )RA470 - 479136 - 145
77chain 'R' and (resid 480 through 494 )RA480 - 494146 - 160
88chain 'R' and (resid 495 through 515 )RA495 - 515161 - 181
99chain 'H' and (resid 1 through 16 )HC1 - 161 - 16
1010chain 'H' and (resid 17 through 100 )HC17 - 10017 - 100
1111chain 'H' and (resid 101 through 125 )HC101 - 125101 - 125
1212chain 'H' and (resid 126 through 140 )HC126 - 140126 - 140
1313chain 'H' and (resid 141 through 209 )HC141 - 209141 - 209
1414chain 'H' and (resid 210 through 222 )HC210 - 222210 - 222
1515chain 'L' and (resid 1 through 18 )LD1 - 181 - 18
1616chain 'L' and (resid 19 through 61 )LD19 - 6119 - 61
1717chain 'L' and (resid 62 through 101 )LD62 - 10162 - 101
1818chain 'L' and (resid 102 through 112 )LD102 - 112102 - 112
1919chain 'L' and (resid 113 through 142 )LD113 - 142113 - 142
2020chain 'L' and (resid 143 through 154 )LD143 - 154143 - 154
2121chain 'L' and (resid 155 through 173 )LD155 - 173155 - 173
2222chain 'L' and (resid 174 through 211 )LD174 - 211174 - 211

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