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- PDB-7wbz: Crystal structure of the SARS-Cov-2 RBD in complex with Fab 2303 -

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Basic information

Entry
Database: PDB / ID: 7wbz
TitleCrystal structure of the SARS-Cov-2 RBD in complex with Fab 2303
Components
  • 2303 heavy chain
  • 2303 light chain
  • Spike protein S1
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / viral protein / 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 / symbiont-mediated suppression of host innate immune response / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / identical protein binding / membrane / 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 speciesSevere acute respiratory syndrome coronavirus 2
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.42 Å
AuthorsXiang, Y. / Ma, B.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Commun Biol / Year: 2022
Title: Conformational flexibility in neutralization of SARS-CoV-2 by naturally elicited anti-SARS-CoV-2 antibodies.
Authors: Ruofan Li / Michael Mor / Bingting Ma / Alex E Clark / Joel Alter / Michal Werbner / Jamie Casey Lee / Sandra L Leibel / Aaron F Carlin / Moshe Dessau / Meital Gal-Tanamy / Ben A Croker / Ye ...Authors: Ruofan Li / Michael Mor / Bingting Ma / Alex E Clark / Joel Alter / Michal Werbner / Jamie Casey Lee / Sandra L Leibel / Aaron F Carlin / Moshe Dessau / Meital Gal-Tanamy / Ben A Croker / Ye Xiang / Natalia T Freund /
Abstract: As new variants of SARS-CoV-2 continue to emerge, it is important to assess the cross-neutralizing capabilities of antibodies naturally elicited during wild type SARS-CoV-2 infection. In the present ...As new variants of SARS-CoV-2 continue to emerge, it is important to assess the cross-neutralizing capabilities of antibodies naturally elicited during wild type SARS-CoV-2 infection. In the present study, we evaluate the activity of nine anti-SARS-CoV-2 monoclonal antibodies (mAbs), previously isolated from convalescent donors infected with the Wuhan-Hu-1 strain, against the SARS-CoV-2 variants of concern (VOC) Alpha, Beta, Gamma, Delta and Omicron. By testing an array of mutated spike receptor binding domain (RBD) proteins, cell-expressed spike proteins from VOCs, and neutralization of SARS-CoV-2 VOCs as pseudoviruses, or as the authentic viruses in culture, we show that mAbs directed against the ACE2 binding site (ACE2bs) are more sensitive to viral evolution compared to anti-RBD non-ACE2bs mAbs, two of which retain their potency against all VOCs tested. At the second part of our study, we reveal the neutralization mechanisms at high molecular resolution of two anti-SARS-CoV-2 neutralizing mAbs by structural characterization. We solve the structures of the Delta-neutralizing ACE2bs mAb TAU-2303 with the SARS-CoV-2 spike trimer and RBD at 4.5 Å and 2.42 Å resolutions, respectively, revealing a similar mode of binding to that between the RBD and ACE2. Furthermore, we provide five additional structures (at resolutions of 4.7 Å, 7.3 Å, 6.4 Å, 3.3 Å, and 6.1 Å) of a second antibody, TAU-2212, complexed with the SARS-CoV-2 spike trimer. TAU-2212 binds an exclusively quaternary epitope, and exhibits a unique, flexible mode of neutralization that involves transitioning between five different conformations, with both arms of the antibody recruited for cross linking intra- and inter-spike RBD subunits. Our study provides additional mechanistic understanding about how antibodies neutralize SARS-CoV-2 and its emerging variants and provides insights on the likelihood of reinfections.
History
DepositionDec 17, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 31, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: 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
A: Spike protein S1
H: 2303 heavy chain
L: 2303 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,8534
Polymers71,6323
Non-polymers2211
Water6,053336
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6060 Å2
ΔGint-23 kcal/mol
Surface area27560 Å2
Unit cell
Length a, b, c (Å)85.134, 149.983, 144.790
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-766-

HOH

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Components

#1: Protein Spike protein S1 / S glycoprotein / E2 / Peplomer protein


Mass: 24600.631 Da / Num. of mol.: 1 / Fragment: receptor binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: S, 2
Production host: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths)
References: UniProt: P0DTC2
#2: Antibody 2303 heavy chain


Mass: 23529.410 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: Antibody 2303 light chain


Mass: 23502.154 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#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 / Feature type: SUBJECT OF INVESTIGATION
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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 336 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.23 Å3/Da / Density % sol: 61.87 %
Crystal growTemperature: 309 K / Method: vapor diffusion, hanging drop
Details: 0.2 M sodium tartrate dibasic dihydrate, 14% (w/v) polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 14, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.4→20.09 Å / Num. obs: 35465 / % possible obs: 99.9 % / Redundancy: 12.1 % / Rmerge(I) obs: 0.19 / Rpim(I) all: 0.057 / Rrim(I) all: 0.199 / Χ2: 0.705 / Net I/σ(I): 2.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.4-2.4410.20.75117450.8190.2360.7890.45298.9
2.44-2.4910.50.71817540.8110.2260.7540.45899.6
2.49-2.5310.90.68317310.8210.2130.7170.47799.9
2.53-2.5811.40.6317460.8760.1920.660.484100
2.58-2.6412.30.56317600.8780.1660.5870.524100
2.64-2.712.70.52117480.9030.1510.5430.55100
2.7-2.7712.70.43717680.9480.1270.4560.57599.9
2.77-2.8412.70.40617620.9430.1180.4230.616100
2.84-2.9312.60.37717550.9280.1120.3940.647100
2.93-3.0212.10.31417710.9570.0940.3280.715100
3.02-3.1311.80.27917490.9640.0850.2920.77100
3.13-3.2512.40.25117800.9750.0750.2620.801100
3.25-3.4130.20617710.9780.060.2150.866100
3.4-3.5812.90.18217520.9820.0540.190.89299.9
3.58-3.812.60.16917790.9860.050.1760.908100
3.8-4.0911.90.14317800.9850.0440.150.919100
4.09-4.512.60.12418040.9910.0370.130.947100
4.5-5.1412.90.11517850.9920.0330.120.879100
5.14-6.4411.80.11818330.990.0360.1240.738100
6.44-2012.10.09918920.9920.030.1030.718100

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7kfv

7kfv


Resolution: 2.42→20.09 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 23.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2201 1848 5.22 %
Rwork0.1821 33534 -
obs0.1841 35382 99.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 119.29 Å2 / Biso mean: 47.1148 Å2 / Biso min: 23.04 Å2
Refinement stepCycle: final / Resolution: 2.42→20.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4798 0 14 336 5148
Biso mean--72.97 47.24 -
Num. residues----625
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.42-2.490.31261390.25862417255695
2.49-2.560.30241110.246126002711100
2.56-2.640.31721330.235725652698100
2.64-2.740.28041360.239225682704100
2.74-2.850.29321460.218925742720100
2.85-2.970.27111010.221326062707100
2.97-3.130.2351560.220125562712100
3.13-3.330.25521410.209525912732100
3.33-3.580.22951710.192525712742100
3.58-3.940.23371900.176425352725100
3.94-4.50.17161500.135626142764100
4.5-5.650.15551300.128626432773100
5.65-20.090.1621440.15962694283899
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)
16.16514.515-3.01147.3207-4.00348.49780.2160.06940.30170.65880.0754-0.4483-1.42710.0107-0.25350.45940.0353-0.00680.26140.01620.4396-1.3661-4.404-12.5444
26.77960.6863.64219.3716-3.04898.0445-0.45860.9951-0.14070.79310.0218-0.5032-1.34912.17830.41430.632-0.2457-0.00730.91370.06470.49599.47-2.67-21.5095
31.0028-1.2811-0.00184.1199-4.55949.86870.00060.3448-0.133-0.0348-0.2202-0.4661-0.38141.16850.19880.3193-0.05340.03030.62540.05110.492410.2451-10.9358-22.3035
41.97640.6199-0.0422.6607-0.78353.55270.04040.12090.0348-0.03950.0007-0.1203-0.21350.2885-0.05050.24750.0138-0.02130.3270.01440.41910.6026-17.5219-12.0516
53.0687-0.4633-1.38152.4736-0.61656.4946-0.0044-0.1445-0.01570.36410.23950.494-0.3703-0.2264-0.27440.31150.05750.02220.28170.07490.4802-8.9574-17.8681-5.342
62.0077-1.9946-0.14742.3603-0.66732.32580.23180.09720.41120.60340.42741.5142-0.1691-0.5579-0.58930.44390.1160.1690.46070.16430.8787-20.6119-25.37840.861
73.10230.0933-0.48032.8574-2.65612.51080.2513-0.0384-0.07150.4126-0.082-0.05110.24860.184-0.27470.4339-0.0516-0.0030.2618-0.00770.38253.5088-15.413-4.4903
87.71762.80326.68172.94643.13328.84721.4453-0.5919-1.16780.59940.088-0.10791.2868-0.4199-1.15270.8386-0.1948-0.08460.56760.17660.57650.3639-3.7594-32.3381
95.9431-2.2172-3.58853.41832.7826.68960.34930.56960.347-0.1916-0.32490.56750.1111-0.8446-0.0010.3176-0.0482-0.04920.3740.08050.5719-8.9982-53.1926-2.7009
105.1606-1.7613-0.84655.9325-0.23960.91320.05240.1275-0.2671-0.14840.07931.3880.038-0.4188-0.14220.29440.0136-0.02610.32890.05920.565-11.6266-42.6259-3.2202
110.49481.1479-0.49833.2158-3.16918.81940.07730.04180.1245-0.24910.01510.1660.321-0.13210.0270.19960.0327-0.0360.2436-0.01690.3902-2.2021-40.0384-3.2375
121.0294-1.4724-1.13735.0959-0.05142.7770.12980.1773-0.0163-0.2198-0.02050.58170.0626-0.1704-0.1260.2113-0.0072-0.06440.27740.03830.4631-6.0814-44.9324-3.5959
132.51370.13650.27195.4058-2.02884.9661-0.0357-0.1746-0.07370.0213-0.0525-0.34370.44760.00860.00140.14250.01880.04140.1958-0.06330.29768.2041-72.593413.0952
14-0.0145-0.50360.42272.0309-0.60041.99640.0882-0.12150.00530.1047-0.0947-0.0295-0.0721-0.08280.03910.2918-0.01050.0440.35050.00840.25473.3076-69.519216.1215
152.74580.1787-1.21023.403-0.30127.8573-0.0854-0.1845-0.1342-0.11540.0870.1550.4524-0.35620.0230.2187-0.02360.03740.3016-0.0060.24152.2128-75.077821.2051
166.6912-1.37915.16845.2893-2.01557.9509-0.0944-0.2753-0.71330.29340.14260.05890.6687-0.0215-0.30430.54670.00550.11350.3750.03110.34474.2933-81.623717.9303
170.28390.9756-0.3614.7179-2.80982.2665-0.093-0.5725-0.1290.9134-0.3802-0.354-1.07230.64970.40720.6726-0.00480.05710.3812-0.0080.40172.5396-38.999723.9903
184.17593.2867-0.93876.9939-2.81554.95650.161-0.3040.15730.715-0.16730.0973-0.18990.2301-0.06410.38380.06550.03890.286-0.00030.32370.3667-33.938212.3523
192.5735-0.8946-0.12853.6735-0.01635.5326-0.1045-0.2250.09610.9984-0.01021.0703-0.0687-0.5204-0.04270.46040.07860.150.31770.01740.5195-10.1621-34.474516.4756
205.54834.7858-4.98845.0676-4.80854.70450.1993-0.3001-0.71861.6803-0.3870.0182-1.29890.20390.04360.77210.0813-0.03970.3564-0.00310.4181-0.2579-30.385920.924
211.92970.7146-1.30344.5054-4.28228.5488-0.0024-0.006-0.2120.5515-0.04240.0931-0.1356-0.1254-0.07010.3461-0.00420.0360.2282-0.03730.3177-0.6227-39.49113.5549
220.66360.140.84811.5988-0.06991.0585-0.2951-0.39570.06691.03960.2688-0.0283-0.04870.2478-0.05270.43170.01690.05170.3145-0.05450.28068.0496-56.511832.8423
235.8899-2.064-1.47084.25213.93549.09360.09450.8729-0.52840.1580.142-0.06311.0243-0.1725-0.24160.3220.01370.0120.3525-0.00250.281216.8825-77.11614.8807
248.0739-4.6094-4.59114.95593.26793.82610.30710.07130.4992-0.0004-0.2931-0.4119-0.21550.0282-0.00990.3401-0.0307-0.00750.36950.05660.197917.004-60.467124.3609
253.3077-0.854-2.9282.46581.78673.4740.18070.25720.45090.2317-0.1651-0.2656-0.1845-0.21580.06480.3622-0.0504-0.00310.35860.04460.249814.1644-59.419717.4609
265.0513-4.7458-5.77734.53545.36746.5557-0.08490.2571-1.15030.1944-0.450.7354-0.235-0.12170.16190.4451-0.01610.01130.43030.00170.49093.5108-58.644427.2959
274.3642-3.2477-1.24094.49660.80031.77960.2546-0.16720.25510.35620.027-0.93150.260.2111-0.29440.2894-0.0439-0.020.38890.0430.290223.3164-68.392322.6333
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 334 through 358 )A334 - 358
2X-RAY DIFFRACTION2chain 'A' and (resid 359 through 370 )A359 - 370
3X-RAY DIFFRACTION3chain 'A' and (resid 371 through 393 )A371 - 393
4X-RAY DIFFRACTION4chain 'A' and (resid 394 through 442 )A394 - 442
5X-RAY DIFFRACTION5chain 'A' and (resid 443 through 469 )A443 - 469
6X-RAY DIFFRACTION6chain 'A' and (resid 470 through 494 )A470 - 494
7X-RAY DIFFRACTION7chain 'A' and (resid 495 through 516 )A495 - 516
8X-RAY DIFFRACTION8chain 'A' and (resid 517 through 527 )A517 - 527
9X-RAY DIFFRACTION9chain 'H' and (resid 1 through 17 )H1 - 17
10X-RAY DIFFRACTION10chain 'H' and (resid 18 through 39 )H18 - 39
11X-RAY DIFFRACTION11chain 'H' and (resid 40 through 59 )H40 - 59
12X-RAY DIFFRACTION12chain 'H' and (resid 60 through 113 )H60 - 113
13X-RAY DIFFRACTION13chain 'H' and (resid 114 through 138 )H114 - 138
14X-RAY DIFFRACTION14chain 'H' and (resid 139 through 179 )H139 - 179
15X-RAY DIFFRACTION15chain 'H' and (resid 180 through 207 )H180 - 207
16X-RAY DIFFRACTION16chain 'H' and (resid 208 through 219 )H208 - 219
17X-RAY DIFFRACTION17chain 'L' and (resid 4 through 21 )L4 - 21
18X-RAY DIFFRACTION18chain 'L' and (resid 22 through 41 )L22 - 41
19X-RAY DIFFRACTION19chain 'L' and (resid 42 through 64 )L42 - 64
20X-RAY DIFFRACTION20chain 'L' and (resid 65 through 78 )L65 - 78
21X-RAY DIFFRACTION21chain 'L' and (resid 79 through 106 )L79 - 106
22X-RAY DIFFRACTION22chain 'L' and (resid 107 through 117 )L107 - 117
23X-RAY DIFFRACTION23chain 'L' and (resid 118 through 132 )L118 - 132
24X-RAY DIFFRACTION24chain 'L' and (resid 133 through 154 )L133 - 154
25X-RAY DIFFRACTION25chain 'L' and (resid 155 through 167 )L155 - 167
26X-RAY DIFFRACTION26chain 'L' and (resid 168 through 178 )L168 - 178
27X-RAY DIFFRACTION27chain 'L' and (resid 179 through 215 )L179 - 215

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