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- PDB-7ps5: Crystal structure of the receptor binding domain of SARS-CoV-2 be... -

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Basic information

Entry
Database: PDB / ID: 7ps5
TitleCrystal structure of the receptor binding domain of SARS-CoV-2 beta variant spike glycoprotein in complex with Beta-47 Fab
Components
  • Beta-47 Fab heavy chain
  • Beta-47 Fab light chain
  • Spike protein S1
KeywordsVIRAL PROTEIN / SARS-COV-2 B.1.1.7 (Alpha) VARIANT / B.1.351 (Beta) VARIANT / P.1 (Gamma) VARIANT / B.1.617.2 (Delta) VARIANT / ANTIBODY / RECEPTOR-BINDING-DOMAIN / SPIKE / NEUTRALISATION / VIRAL PROTEIN/IMMUNE SYSTEM / IMMUNE SYSTEM / VIRAL PROTEIN-IMMUNE SYSTEM COMPLEX
Function / homology
Function and homology information


Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell ...Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / membrane fusion / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / membrane / identical protein binding / plasma membrane
Similarity search - Function
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 ...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
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Severe acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.14 Å
AuthorsZhou, D. / Ren, J. / Stuart, D.I.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/ N00065X/1 United Kingdom
CAMS Innovation Fund for Medical Sciences (CIFMS)2018-I2M-2-002 United Kingdom
CitationJournal: Cell Host Microbe / Year: 2022
Title: The antibody response to SARS-CoV-2 Beta underscores the antigenic distance to other variants.
Authors: Chang Liu / Daming Zhou / Rungtiwa Nutalai / Helen M E Duyvesteyn / Aekkachai Tuekprakhon / Helen M Ginn / Wanwisa Dejnirattisai / Piyada Supasa / Alexander J Mentzer / Beibei Wang / James ...Authors: Chang Liu / Daming Zhou / Rungtiwa Nutalai / Helen M E Duyvesteyn / Aekkachai Tuekprakhon / Helen M Ginn / Wanwisa Dejnirattisai / Piyada Supasa / Alexander J Mentzer / Beibei Wang / James Brett Case / Yuguang Zhao / Donal T Skelly / Rita E Chen / Sile Ann Johnson / Thomas G Ritter / Chris Mason / Tariq Malik / Nigel Temperton / Neil G Paterson / Mark A Williams / David R Hall / Daniel K Clare / Andrew Howe / Philip J R Goulder / Elizabeth E Fry / Michael S Diamond / Juthathip Mongkolsapaya / Jingshan Ren / David I Stuart / Gavin R Screaton /
Abstract: Alpha-B.1.1.7, Beta-B.1.351, Gamma-P.1, and Delta-B.1.617.2 variants of SARS-CoV-2 express multiple mutations in the spike protein (S). These may alter the antigenic structure of S, causing escape ...Alpha-B.1.1.7, Beta-B.1.351, Gamma-P.1, and Delta-B.1.617.2 variants of SARS-CoV-2 express multiple mutations in the spike protein (S). These may alter the antigenic structure of S, causing escape from natural or vaccine-induced immunity. Beta is particularly difficult to neutralize using serum induced by early pandemic SARS-CoV-2 strains and is most antigenically separated from Delta. To understand this, we generated 674 mAbs from Beta-infected individuals and performed a detailed structure-function analysis of the 27 most potent mAbs: one binding the spike N-terminal domain (NTD), the rest the receptor-binding domain (RBD). Two of these RBD-binding mAbs recognize a neutralizing epitope conserved between SARS-CoV-1 and -2, while 18 target mutated residues in Beta: K417N, E484K, and N501Y. There is a major response to N501Y, including a public IgVH4-39 sequence, with E484K and K417N also targeted. Recognition of these key residues underscores why serum from Beta cases poorly neutralizes early pandemic and Delta viruses.
History
DepositionSep 22, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 15, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 22, 2021Group: Database references / Source and taxonomy / Structure summary
Category: entity / entity_src_gen ...entity / entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity_src_gen.gene_src_common_name ..._entity.pdbx_description / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_gene / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_db_accession
Revision 1.2Dec 29, 2021Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.3Jan 26, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.year
Revision 1.4Jan 31, 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
H: Beta-47 Fab heavy chain
L: Beta-47 Fab light chain
E: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,6285
Polymers71,6763
Non-polymers1,9522
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7270 Å2
ΔGint-7 kcal/mol
Surface area30170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.101, 114.409, 168.972
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Antibody Beta-47 Fab heavy chain


Mass: 24438.500 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody Beta-47 Fab light chain


Mass: 23591.221 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Protein Spike protein S1


Mass: 23646.551 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: S, 2 / Production host: Homo sapiens (human) / References: UniProt: P0DTC2
#4: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1056.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-3-4/a4-b1_a6-f1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#5: Polysaccharide alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 894.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpb1-3DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-4/a4-b1_a6-e1_b3-c1_c6-d1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(3+1)][b-D-Manp]{[(6+1)][a-D-Manp]{}}}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
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: 5.44 Å3/Da / Density % sol: 77.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Potassium chloride, 0.1 M Tris pH 8.0 and 15% (w/v) PEG 2000 MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97627 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 14, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97627 Å / Relative weight: 1
ReflectionResolution: 3.14→60 Å / Num. obs: 27125 / % possible obs: 100 % / Redundancy: 12.2 % / Biso Wilson estimate: 115.02 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.229 / Rpim(I) all: 0.068 / Net I/σ(I): 7.8
Reflection shellResolution: 3.14→3.2 Å / Mean I/σ(I) obs: 0.3 / Num. unique obs: 1313 / CC1/2: 0.365

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Processing

Software
NameVersionClassification
GDA1.19_4092data collection
PHENIX1.19_4092refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7ORB

7orb


Resolution: 3.14→57.35 Å / SU ML: 0.7635 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 35.8284
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2738 1307 4.92 %
Rwork0.2255 25277 -
obs0.2277 26584 98.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 129.65 Å2
Refinement stepCycle: LAST / Resolution: 3.14→57.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4869 0 131 0 5000
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00325126
X-RAY DIFFRACTIONf_angle_d0.53636975
X-RAY DIFFRACTIONf_chiral_restr0.0414808
X-RAY DIFFRACTIONf_plane_restr0.0046882
X-RAY DIFFRACTIONf_dihedral_angle_d10.73691878
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.14-3.270.42681130.4512400X-RAY DIFFRACTION84.61
3.27-3.420.45221620.39792771X-RAY DIFFRACTION99.9
3.42-3.60.40181510.32912801X-RAY DIFFRACTION99.8
3.6-3.820.31171470.28772820X-RAY DIFFRACTION99.7
3.82-4.120.2971370.2532853X-RAY DIFFRACTION100
4.12-4.530.23631570.19512816X-RAY DIFFRACTION99.8
4.53-5.190.23641580.17872867X-RAY DIFFRACTION100
5.19-6.540.26031300.20542915X-RAY DIFFRACTION99.97
6.54-57.350.2351520.18733034X-RAY DIFFRACTION99.84
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)
16.204492940722.862399872121.965331552084.456513640852.836152487715.667330118430.382303590985-0.425881109692-0.6895873509280.565082311480.148867692995-0.203706135251.23933200831-0.0441436686918-0.3958788148950.881848931670.0846278339747-0.02995209781240.705051395675-0.003556006942610.597724314025-14.037936103312.34465857813.87276799461
27.48112923272.097870343761.884176989595.574900636452.584246145757.51479109709-0.02452362296170.1181067087510.273863786560.58413286437-0.04866177574630.3457697714940.12463455257-0.05841461957190.0481204813580.8835894739740.07145570655720.04833441844710.8513549776990.02113674881870.730673116454-13.796117214818.76821164792.66300456484
35.890391026390.278337509996-4.208477737381.407899160740.7636905502925.996708796180.3011359526020.9892859776961.1929112904-0.780023513627-0.12943317702-0.08049124668060.392897929403-1.24617876544-0.4655706443721.420372522280.05305897567980.08168365885450.7389678319810.09656796256260.967429657609-29.39844972934.16500372858-29.4712749168
45.74189549207-0.227888131628-2.682107804241.163129327871.502575708768.382456658150.379848418528-0.5436019660030.1276501137080.1299255758610.0811832031352-0.1249323944520.9390671806710.697455053566-0.3861980571791.57783284989-0.007878893741120.01878580876571.12223750881-0.09436294461310.976771243885-22.9671965911.28914928483-27.7252822616
55.826505869190.0530345528617-0.2446289849413.461165006691.65042017330.6916615125591.015678536990.03778557465150.1613429530071.106116932280.5091488479611.2322270158-1.00546485562-0.328079068921-0.8311710887281.669044883860.001976558634620.08909285524541.05330225451-0.2876403822991.15164938577-29.9895078547-4.42680300767-32.563114793
64.844352777593.064615836150.8621043201655.82854796722-1.60684886572.47332099223-1.169919832532.05276124653-0.621488172157-0.6731360799720.4579447107950.4518787522990.283867902328-0.2949456951110.8558026718231.26899664678-0.3005587495910.0895816172391.374622379740.05687091487970.812122005177-1.2309519908125.299440642-18.9703623042
75.584798918572.604918967550.3642145076465.644788018210.2314915993366.6140400177-0.2817014096631.018560178680.039592599904-0.3533473742840.430310852245-0.949036315617-0.4296613347061.58186625105-0.1977161575731.0780750903-0.22755363840.06290259126211.40836853518-0.04952526012070.8561979520482.4743799128223.7407225515-8.73855633772
84.934764418350.254477365862-4.870373618443.508043081471.079001134638.32870665215-0.2125421185850.770697097246-0.302154792943-0.4781271853290.283067310369-0.2234259214340.3026051137510.196967741969-0.2323778806141.36756476962-0.0650831797156-0.08265127688311.25023061015-0.05783158256050.958152212951-1.7584225182421.76397486-11.1258217936
90.4977615350860.581555957041.051339205310.7941273627411.396727603142.42553872596-1.070513448431.26665873603-0.351241139219-0.9022535737441.06548944308-0.756607219257-1.186072093433.30175569485-0.4123241870111.57868631086-0.273374167532-0.03761470133312.22531338674-0.229576715890.927283965682-3.6821428453216.3905597737-31.645059654
107.08497283301-0.155908135823-0.5255831382860.0444031268931-1.909984601524.521614285280.1066869723610.0244270940407-0.206550974348-0.217873972722-0.01384007421480.08159931756670.1666893990010.4464163985220.1049981169971.37233155168-0.04990385596230.02302636720960.846427362857-0.1758205222480.849539646541-25.016834592313.2521335644-34.1800470394
119.75673603228-2.401001061832.973970523650.649469176475-2.262377287576.16238660887-0.241479305005-0.5527466807940.18987150619-0.2872875467520.103589073474-0.0471651389504-0.005721843291150.519870476620.4255083534831.68736787597-0.0548768465134-0.007049538781781.05635990142-0.169931624541.01342558089-18.35810675115.602626466-30.1692513674
123.60149426406-2.59219848489-1.904991660582.517810867610.5674826720832.855622778130.3757269846520.973461646647-0.464582533248-0.562777131543-0.08562653983560.007797799146050.0924475727277-0.0132548408802-0.4569044671031.44068010927-0.02550055647240.006463122256381.08470862241-0.06775269589520.790133612225-29.164316295917.3111636463-38.5758045715
133.04996646471-1.040380285960.627058306774.18575223157-2.113818944454.95259026235-0.249733791076-0.5996428632870.351967021191.41347992856-0.1095904045790.518169874279-0.9768460611820.269071345819-0.267771073562.038403811060.0977317598070.0873184860911.17637905225-0.008738957148110.843122556713-4.3660101174627.898138809147.9364892342
145.85429277859-0.1240054314862.381107096875.98305187787-0.4305689401173.17786170850.574514356628-0.505670907822-0.7526619497351.41360262480.1698631503650.0494719219875-0.3395079464250.613553000332-0.3775260882431.580267144190.08734677165030.06790610635221.151721870770.1202641760430.997349426676-3.7199819046516.103006927546.3116211585
153.187022688871.60752881131-0.3183590361712.85031068083-1.744386958848.327820543870.1253140241150.0226649789616-0.2176281417640.705439006320.077998306969-0.1069025289750.07302763563850.685717082158-0.4005661764771.026033071840.1898178585770.01940153634390.82460345635-0.02513533110270.836664678023-2.2845173737722.967234538429.7908376282
164.24754285411.38967925206-2.378341886012.12458192584-0.7745673711324.968432437260.400412490273-0.199191638756-0.1001233972690.6481198462210.2093666933710.103607486696-0.404865841453-0.196094467812-0.3846748453441.266253483550.1387207356920.0518673669850.781767657294-0.06421503898021.08310245336-4.8557749162624.120771286131.8808132806
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'H' and (resid 1 through 39 )HA1 - 391 - 39
22chain 'H' and (resid 40 through 121 )HA40 - 12140 - 121
33chain 'H' and (resid 122 through 144 )HA122 - 144122 - 142
44chain 'H' and (resid 145 through 213 )HA145 - 213143 - 211
55chain 'H' and (resid 214 through 226 )HA214 - 226212 - 224
66chain 'L' and (resid 1 through 18 )LB1 - 181 - 18
77chain 'L' and (resid 19 through 76 )LB19 - 7619 - 76
88chain 'L' and (resid 77 through 103 )LB77 - 10377 - 103
99chain 'L' and (resid 104 through 114 )LB104 - 114104 - 114
1010chain 'L' and (resid 115 through 151 )LB115 - 151115 - 151
1111chain 'L' and (resid 152 through 175 )LB152 - 175152 - 175
1212chain 'L' and (resid 176 through 215 )LB176 - 215176 - 215
1313chain 'E' and (resid 333 through 365 )EC333 - 3651 - 33
1414chain 'E' and (resid 366 through 409 )EC366 - 40934 - 77
1515chain 'E' and (resid 410 through 479 )EC410 - 47978 - 147
1616chain 'E' and (resid 480 through 525 )EC480 - 525148 - 193

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