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- PDB-7qt0: Antibody FenAb136 - fentanyl complex -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 7qt0
TitleAntibody FenAb136 - fentanyl complex
Components
  • Antibody heavy chain
  • Antibody light chain
KeywordsIMMUNE SYSTEM / antibody
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Chem-FD0
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.07 Å
AuthorsZeelen, J.P. / Straaten van, M. / Stebbins, C.E.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Cell Rep / Year: 2023
Title: A trypanosome-derived immunotherapeutics platform elicits potent high-affinity antibodies, negating the effects of the synthetic opioid fentanyl.
Authors: Triller, G. / Vlachou, E.P. / Hashemi, H. / van Straaten, M. / Zeelen, J.P. / Kelemen, Y. / Baehr, C. / Marker, C.L. / Ruf, S. / Svirina, A. / Chandra, M. / Urban, K. / Gkeka, A. / Kruse, S. ...Authors: Triller, G. / Vlachou, E.P. / Hashemi, H. / van Straaten, M. / Zeelen, J.P. / Kelemen, Y. / Baehr, C. / Marker, C.L. / Ruf, S. / Svirina, A. / Chandra, M. / Urban, K. / Gkeka, A. / Kruse, S. / Baumann, A. / Miller, A.K. / Bartel, M. / Pravetoni, M. / Stebbins, C.E. / Papavasiliou, F.N. / Verdi, J.P.
History
DepositionJan 14, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 24, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Antibody heavy chain
B: Antibody light chain
C: Antibody heavy chain
D: Antibody light chain
E: Antibody heavy chain
F: Antibody light chain
G: Antibody heavy chain
H: Antibody light chain
I: Antibody heavy chain
J: Antibody light chain
K: Antibody heavy chain
L: Antibody light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)291,73218
Polymers288,02612
Non-polymers3,7066
Water23,9241328
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)182.982, 105.843, 172.775
Angle α, β, γ (deg.)90.000, 112.240, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody
Antibody heavy chain


Mass: 24308.229 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): Freestyle 293 / Production host: Homo sapiens (human)
#2: Antibody
Antibody light chain


Mass: 23696.059 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): Freestyle 293 / Production host: Homo sapiens (human)
#3: Chemical
ChemComp-FD0 / 2-[2-[2-[2-[[5-oxidanylidene-5-[2-[4-[phenyl(propanoyl)amino]piperidin-1-yl]ethylamino]pentanoyl]amino]ethanoylamino]ethanoylamino]ethanoylamino]ethanoic acid


Mass: 617.694 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C29H43N7O8 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1328 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.69 Å3/Da / Density % sol: 54.25 %
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 2.0m M (NH4)2SO4, 0.1 M ADA/NaOH, 10 % Ethanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Feb 19, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.07→54.52 Å / Num. obs: 181970 / % possible obs: 97.51 % / Redundancy: 2 % / Biso Wilson estimate: 35.64 Å2 / CC1/2: 0.987 / Rmerge(I) obs: 0.0637 / Net I/σ(I): 7.29
Reflection shellResolution: 2.07→2.14 Å / Redundancy: 2 % / Rmerge(I) obs: 0.5982 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 17881 / CC1/2: 0.584 / % possible all: 96.49

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5H2B
Resolution: 2.07→54.52 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 34.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2819 3884 1.1 %
Rwork0.2417 350507 -
obs0.2422 181970 96.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 114.71 Å2 / Biso mean: 45.8176 Å2 / Biso min: 24.74 Å2
Refinement stepCycle: final / Resolution: 2.07→54.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19532 0 172 1328 21032
Biso mean--46.12 45.4 -
Num. residues----2558
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.07-2.10.42171340.35741207195
2.1-2.120.36881210.34881238295
2.12-2.150.41661310.3361235395
2.15-2.180.40071470.32931228995
2.18-2.210.32271260.32061234996
2.21-2.240.37621480.31561247496
2.24-2.280.33451510.32111233696
2.28-2.320.34741230.3051254996
2.32-2.360.31081390.30931246297
2.36-2.40.37341430.311257697
2.4-2.440.35651440.30051242497
2.44-2.490.30511380.29821250397
2.49-2.550.2951240.2951252997
2.55-2.610.31281520.28391249497
2.61-2.670.32321430.28171254097
2.67-2.750.35131470.27291263597
2.75-2.830.31971340.28061257398
2.83-2.920.37021390.27151263698
2.92-3.020.35251450.2721268598
3.02-3.140.31141460.25161254598
3.14-3.290.30781310.24531265698
3.29-3.460.29671310.22531262798
3.46-3.680.21791480.21411264998
3.68-3.960.25751410.20141257198
3.96-4.360.20771390.18431264898
4.36-4.990.1851380.17061257997
4.99-6.280.25091350.20211270798
6.28-54.520.22851460.21951266598
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)
16.93212.9686-5.87483.3304-3.00184.971-0.1288-0.7308-0.3136-0.3475-0.0785-0.23780.39350.69490.38390.5076-0.0241-0.03250.3550.04940.4288-40.509-4.66256.237
22.2135-0.1989-0.67861.48890.1257-0.02490.03340.31360.2821-0.38860.08990.14390.0564-0.0308-0.13460.6124-0.0288-0.03810.40120.09210.3824-47.0150.74751.82
31.41610.26490.88131.18041.23754.1139-0.05420.02250.05830.23880.0101-0.10580.2035-0.03970.03910.58030.01150.10970.1970.03650.408-18.5821.37765.003
42.38681.26981.52042.7735-0.82062.1246-0.08460.06440.5894-0.098-0.05540.5574-0.234-0.03520.16980.50640.02760.02290.24730.04340.5422-48.25518.4464.879
51.71850.845-0.42620.8514-0.07450.25660.05170.05430.341-0.04330.00940.1091-0.07520.0008-0.04720.64140.04020.09880.25530.04850.4675-27.78417.02963.711
66.5848-0.3701-2.61542.4389-0.3294.0580.0121-0.1642-0.0823-0.1803-0.0023-0.382-0.07030.4328-0.00830.495-0.00890.01960.2580.05580.3642-5.22915.67861.621
72.28631.80681.50697.925.35396.31460.33550.07020.0350.5928-0.09970.24120.2198-0.6816-0.22550.5825-0.02960.11310.30130.03780.395-23.261-25.84648.169
81.7186-0.52350.50441.8762-0.64091.2178-0.01080.20540.0563-0.46060.0143-0.25620.1299-0.0379-0.01390.6287-0.00220.19220.2840.03470.3773-14.144-20.67943.247
92.39042.55340.88997.22393.46233.93650.07580.2675-0.2034-0.25930.0546-0.78120.1541-0.2136-0.15490.58550.00960.17820.23260.01990.4003-14.317-27.55545.123
101.9150.7550.00230.4568-0.48580.7763-0.23520.0950.0984-0.11180.10160.09410.05220.010.16420.67650.02410.17540.25370.00680.43-17.032-27.84752.794
116.48621.56025.17090.92181.77344.73670.3547-0.813-0.8221-0.2130.4251-0.35190.1384-0.67-0.50860.50960.07190.10040.30.00110.4137-24.939-51.84668.292
122.7674-0.05182.36531.1924-1.59285.5627-0.3182-0.0648-0.0496-0.12470.0754-0.18530.0875-0.0470.24590.49330.00610.09210.1969-0.01560.3903-24.498-44.14165.208
131.6311-2.81862.84947.2856-6.68629.24630.61420.1973-0.3176-0.8489-0.33550.47041.43110.9628-0.08580.64930.06130.20840.4354-0.00890.51845.979-36.87353.112
143.16550.1762-0.33442.2844-0.97532.119-0.0958-0.0669-0.171-0.09-0.0509-0.26760.17020.16950.16590.55380.03860.13820.29170.03580.43523.112-27.96855.831
150.57250.5467-0.23130.4194-0.57110.72640.08250.0126-0.1609-0.0359-0.1129-0.1986-0.00240.14110.01650.54130.04880.18390.3094-0.01710.3823-10.403-44.38458.33
164.35230.91751.17670.2019-0.0231.45170.00990.1847-0.6592-0.22850.0596-0.27680.29780.11-0.07640.7210.090.19860.26730.02530.5907-16.256-60.73562.639
171.8258-1.96360.65597.6192-0.88670.34440.0850.2597-0.0484-0.161-0.06530.0471-0.0521-0.4092-0.05630.45260.01370.06970.39220.02110.3363-14.603-73.52229.357
180.7761-0.14620.4711.9899-0.82760.67650.0794-0.09570.08290.24220.09010.2073-0.0987-0.2072-0.16570.5840.0270.15550.32180.02450.3925-10.672-75.74336.927
193.6263-1.74020.86833.37780.73020.8728-0.48270.67340.41640.23630.38240.1209-0.0850.01780.0460.5312-0.02190.01310.30290.00710.3177-1.582-47.12813.526
205.38021.5453-1.35641.4099-1.36762.48-0.1616-0.1198-0.2640.23120.2176-0.0761-0.07960.0727-0.04210.42040.04840.05070.20980.0010.2976-4.009-55.04316.501
219.16863.0527-6.52473.8501-2.00154.80240.0857-0.25430.83320.22190.1080.2563-0.20390.1001-0.23510.7628-0.0213-0.11340.3731-0.00330.488110.209-62.45945.718
227.41963.2081-4.23148.2311-1.43134.1986-0.0314-0.77410.32580.95180.09550.67760.33120.2221-0.06310.5559-0.01610.00160.40120.02510.28467.958-71.84952.553
234.8332-1.64521.69082.2881-2.12874.13070.00870.27580.22270.8338-0.27850.1534-0.62590.12440.22670.53360.00210.10540.21470.05280.34574.421-70.19136.661
243.86341.7911-0.24135.9524-1.06964.189-0.3983-0.2515-0.24670.56720.0703-0.4480.53950.53140.28660.51420.05970.0780.25210.02540.347713.167-75.1842.898
252.35722.6459-2.32952.8976-1.58793.0801-0.0126-0.0159-0.08060.38280.0348-0.0785-0.21210.1014-0.07510.51280.01610.02850.31930.01290.33857.777-64.51840.045
263.3346-0.25910.13762.36370.0360.248-0.3015-0.16820.60180.77050.20880.0697-0.6678-0.00550.03150.780.02860.04370.2513-0.01680.3998-1.02-39.521.894
277.043-4.95881.64835.1926-2.10141.39980.0528-0.3483-0.03960.46820.07230.0892-0.3786-0.3635-0.07340.7229-0.01290.13430.3411-0.02210.31473.687-48.55929.089
284.48540.13981.9633.2942-0.85983.7882-0.0761-0.03920.50350.53560.0590.5495-0.6297-0.34470.09830.79040.1220.13520.31340.04620.5888-10.439-35.93719.157
291.8211-2.50251.08814.5507-3.0062.6413-0.43360.07950.7050.17280.0977-0.0627-0.77240.27370.35650.9923-0.1338-0.01180.31170.01950.64124.221-33.10821.293
303.7046-0.9182.0073.52251.9682.8614-0.10370.09420.030.42540.1920.3516-0.611-0.083-0.19680.403-0.06310.08940.37920.03290.3577-23.90910.43815.833
310.77230.0071.35621.4801-0.53571.68420.0473-0.2868-0.1470.05390.20110.34270.4835-0.3664-0.22550.4451-0.09970.06020.49020.10710.3974-29.735.73710.105
322.8992-0.1972-1.58773.73820.1476.12490.3977-0.51690.28050.12520.7355-0.63890.54860.6804-0.26450.65290.0298-0.11990.2332-0.2230.50799.5182.67623.209
335.7357-1.2531-2.12560.68611.00292.49320.0961-0.00730.0746-0.07120.0355-0.08690.1722-0.0806-0.110.5578-0.05750.01760.20380.0340.3184-0.9465.51220.045
342.8574-0.71670.25941.9784-1.09761.45230.3025-0.2868-0.6406-0.4410.07530.49140.6109-0.1417-0.30640.857-0.1301-0.12210.36370.07180.4991-22.265-12.0950.491
351.3391-0.23390.89552.1041.29564.3040.026-0.1013-0.1332-0.01210.1224-0.12050.18020.1453-0.13790.6824-0.00790.07860.25780.03070.35793.23-9.13526.61
363.29671.45880.24052.5321.24750.9056-0.2272-0.103-0.14950.45440.0758-0.35060.0580.16780.16480.58170.0058-0.07130.3390.07890.3335-13.331-38.991109.003
372.45342.3246-0.05517.22131.30762.15630.1041-0.1683-0.49270.10.0039-0.58490.1828-0.0401-0.10460.34840.0159-0.03260.25680.03820.2352-12.315-37.065100.303
380.9977-0.7703-0.44083.00380.5111.12930.2292-0.0170.1843-0.1254-0.0882-0.2164-0.1952-0.1562-0.14740.3980.00710.06490.26930.01870.3635-4.434-19.27587.307
392.3749-1.0501-1.12722.0531-0.31488.9075-0.1477-0.4333-0.1065-0.16350.1715-0.51240.56951.5582-0.06790.59060.11980.13150.5030.0810.79955.806-50.12290.913
403.5031-0.7415-0.09872.52230.90174.821-0.2569-0.1093-0.2731-0.13480.0382-0.33620.42910.36810.13910.46990.04810.08430.31270.07360.5097-3.997-51.66791.028
410.25720.00620.05754.6668-0.2960.34750.1191-0.15070.17210.0913-0.0108-0.6418-0.13180.2381-0.1110.5239-0.02960.09230.44660.02760.67888.612-25.68988.005
421.23240.1636-0.74945.08032.95142.86410.2269-0.06180.0787-0.6841-0.0148-0.8499-0.56630.2709-0.23860.508-0.03790.09490.43320.08680.799812.831-16.57883.148
432.3413-2.8561.855.4154-1.03042.1007-0.16910.2059-0.45730.0330.0495-0.19680.34580.48990.12640.41340.07650.19040.543-0.03140.4532-60.296-14.916-7.024
440.2225-0.43950.66342.2258-0.0892.0096-0.06710.08050.0371-0.08440.0455-0.3704-0.05570.59380.02560.2891-0.0030.12890.5238-0.00670.393-58.794-6.109-5.91
452.41110.5851-1.67964.11010.75185.4750.18010.0399-0.01740.4414-0.0816-0.19940.4246-0.0784-0.05660.36220.0226-0.0910.268-0.02210.279-65.561-28.95214.928
467.72974.5608-7.13953.6471-4.89898.1744-0.1976-0.04270.6565-0.40260.41980.16830.51580.9751-0.27530.4888-0.1290.03860.7621-0.09050.4341-56.153.71318.36
473.97990.6986-0.4691.9134-0.60072.78620.19990.05720.13760.16990.0806-0.1167-0.44840.7704-0.23710.3461-0.1338-0.0090.4408-0.04660.3284-63.0216.52110.366
480.61041.3757-1.05012.4969-2.94977.03810.0763-0.01680.15430.2470.05210.0287-0.16670.7629-0.15530.3559-0.06490.01140.4455-0.02710.4348-59.745-0.59915.262
493.6863-2.2581-0.27926.23830.87742.76810.086-0.02350.05960.2368-0.0446-0.61490.56230.5436-0.03880.54610.0564-0.09320.4485-0.00870.3603-55.312-30.8226.344
501.7879-1.1638-0.29794.94781.90563.34770.03980.0465-0.12110.3909-0.047-0.35070.58850.3192-0.01040.50390.0368-0.13840.48-0.03450.3769-54.423-29.1827.574
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1:12 )A1 - 12
2X-RAY DIFFRACTION2( CHAIN A AND RESID 13:126 )A13 - 126
3X-RAY DIFFRACTION3( CHAIN A AND RESID 127:220 )A127 - 220
4X-RAY DIFFRACTION4( CHAIN B AND RESID 1:61 )B1 - 61
5X-RAY DIFFRACTION5( CHAIN B AND RESID 62:174 )B62 - 174
6X-RAY DIFFRACTION6( CHAIN B AND RESID 175:211 )B175 - 211
7X-RAY DIFFRACTION7( CHAIN C AND RESID 1:25 )C1 - 25
8X-RAY DIFFRACTION8( CHAIN C AND RESID 26:83 )C26 - 83
9X-RAY DIFFRACTION9( CHAIN C AND RESID 84:101 )C84 - 101
10X-RAY DIFFRACTION10( CHAIN C AND RESID 102:126 )C102 - 126
11X-RAY DIFFRACTION11( CHAIN C AND RESID 127:152 )C127 - 152
12X-RAY DIFFRACTION12( CHAIN C AND RESID 153:219 )C153 - 219
13X-RAY DIFFRACTION13( CHAIN D AND RESID 1:18 )D1 - 18
14X-RAY DIFFRACTION14( CHAIN D AND RESID 19:90 )D19 - 90
15X-RAY DIFFRACTION15( CHAIN D AND RESID 91:128 )D91 - 128
16X-RAY DIFFRACTION16( CHAIN D AND RESID 129:212 )D129 - 212
17X-RAY DIFFRACTION17( CHAIN E AND RESID 1:25 )E1 - 25
18X-RAY DIFFRACTION18( CHAIN E AND RESID 26:126 )E26 - 126
19X-RAY DIFFRACTION19( CHAIN E AND RESID 127:152 )E127 - 152
20X-RAY DIFFRACTION20( CHAIN E AND RESID 153:219 )E153 - 219
21X-RAY DIFFRACTION21( CHAIN F AND RESID 1:18 )F1 - 18
22X-RAY DIFFRACTION22( CHAIN F AND RESID 19:32 )F19 - 32
23X-RAY DIFFRACTION23( CHAIN F AND RESID 33:48 )F33 - 48
24X-RAY DIFFRACTION24( CHAIN F AND RESID 49:75 )F49 - 75
25X-RAY DIFFRACTION25( CHAIN F AND RESID 76:113 )F76 - 113
26X-RAY DIFFRACTION26( CHAIN F AND RESID 114:155 )F114 - 155
27X-RAY DIFFRACTION27( CHAIN F AND RESID 156:174 )F156 - 174
28X-RAY DIFFRACTION28( CHAIN F AND RESID 175:188 )F175 - 188
29X-RAY DIFFRACTION29( CHAIN F AND RESID 189:211 )F189 - 211
30X-RAY DIFFRACTION30( CHAIN G AND RESID 1:16 )G1 - 16
31X-RAY DIFFRACTION31( CHAIN G AND RESID 17:126 )G17 - 126
32X-RAY DIFFRACTION32( CHAIN G AND RESID 127:141 )G127 - 141
33X-RAY DIFFRACTION33( CHAIN G AND RESID 142:220 )G142 - 220
34X-RAY DIFFRACTION34( CHAIN H AND RESID 1:102 )H1 - 102
35X-RAY DIFFRACTION35( CHAIN H AND RESID 103:212 )H103 - 212
36X-RAY DIFFRACTION36( CHAIN I AND RESID 1:91 )I1 - 91
37X-RAY DIFFRACTION37( CHAIN I AND RESID 92:126 )I92 - 126
38X-RAY DIFFRACTION38( CHAIN I AND RESID 127:219 )I127 - 219
39X-RAY DIFFRACTION39( CHAIN J AND RESID 1:18 )J1 - 18
40X-RAY DIFFRACTION40( CHAIN J AND RESID 19:90 )J19 - 90
41X-RAY DIFFRACTION41( CHAIN J AND RESID 91:163 )J91 - 163
42X-RAY DIFFRACTION42( CHAIN J AND RESID 164:212 )J164 - 212
43X-RAY DIFFRACTION43( CHAIN K AND RESID 1:25 )K1 - 25
44X-RAY DIFFRACTION44( CHAIN K AND RESID 26:126 )K26 - 126
45X-RAY DIFFRACTION45( CHAIN K AND RESID 127:219 )K127 - 219
46X-RAY DIFFRACTION46( CHAIN L AND RESID 1:18 )L1 - 18
47X-RAY DIFFRACTION47( CHAIN L AND RESID 19:75 )L19 - 75
48X-RAY DIFFRACTION48( CHAIN L AND RESID 76:113 )L76 - 113
49X-RAY DIFFRACTION49( CHAIN L AND RESID 114:155 )L114 - 155
50X-RAY DIFFRACTION50( CHAIN L AND RESID 156:211 )L156 - 211

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