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- PDB-7l1d: Crystal structure of human 21LT2-2 TCR bound to HLA-A*03:01 in co... -

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Basic information

Entry
Database: PDB / ID: 7l1d
TitleCrystal structure of human 21LT2-2 TCR bound to HLA-A*03:01 in complex with a mutant PIK3CA peptide
Components
  • (T cell receptor, ...) x 2
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, A alpha chain
  • Mutant PIK3CA peptide
KeywordsIMMUNE SYSTEM / T cell receptor / peptide major histocompatibility complex
Function / homology
Function and homology information


response to muscle inactivity / regulation of actin filament organization / negative regulation of actin filament depolymerization / response to L-leucine / response to butyrate / IRS-mediated signalling / phosphatidylinositol 3-kinase complex / PI3K events in ERBB4 signaling / autosome genomic imprinting / cellular response to hydrostatic pressure ...response to muscle inactivity / regulation of actin filament organization / negative regulation of actin filament depolymerization / response to L-leucine / response to butyrate / IRS-mediated signalling / phosphatidylinositol 3-kinase complex / PI3K events in ERBB4 signaling / autosome genomic imprinting / cellular response to hydrostatic pressure / regulation of cellular respiration / Activated NTRK2 signals through PI3K / negative regulation of fibroblast apoptotic process / Activated NTRK3 signals through PI3K / phosphatidylinositol 3-kinase complex, class IB / positive regulation of protein localization to membrane / vasculature development / 1-phosphatidylinositol-4-phosphate 3-kinase activity / Signaling by cytosolic FGFR1 fusion mutants / Co-stimulation by ICOS / cardiac muscle cell contraction / phosphatidylinositol 3-kinase complex, class IA / Nephrin family interactions / Signaling by LTK in cancer / anoikis / phosphatidylinositol-3-phosphate biosynthetic process / relaxation of cardiac muscle / Signaling by LTK / MET activates PI3K/AKT signaling / PI3K/AKT activation / 1-phosphatidylinositol-4,5-bisphosphate 3-kinase activity / phosphatidylinositol-4,5-bisphosphate 3-kinase / vascular endothelial growth factor signaling pathway / phosphatidylinositol 3-kinase / positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / TAP complex binding / Golgi medial cisterna / 1-phosphatidylinositol-3-kinase activity / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of CD8-positive, alpha-beta T cell proliferation / Signaling by ALK / PI-3K cascade:FGFR3 / Erythropoietin activates Phosphoinositide-3-kinase (PI3K) / negative regulation of macroautophagy / PI-3K cascade:FGFR2 / response to dexamethasone / PI-3K cascade:FGFR4 / phosphatidylinositol-mediated signaling / CD8 receptor binding / PI-3K cascade:FGFR1 / antigen processing and presentation of exogenous peptide antigen via MHC class I / beta-2-microglobulin binding / phosphatidylinositol phosphate biosynthetic process / Synthesis of PIPs at the plasma membrane / endoplasmic reticulum exit site / TAP binding / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / RET signaling / protection from natural killer cell mediated cytotoxicity / negative regulation of anoikis / PI3K events in ERBB2 signaling / Interleukin-3, Interleukin-5 and GM-CSF signaling / insulin receptor substrate binding / PI3K Cascade / intercalated disc / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / regulation of multicellular organism growth / protein kinase activator activity / CD28 dependent PI3K/Akt signaling / Role of LAT2/NTAL/LAB on calcium mobilization / RAC2 GTPase cycle / Interleukin receptor SHC signaling / positive regulation of TOR signaling / Role of phospholipids in phagocytosis / GAB1 signalosome / adipose tissue development / phagocytosis / endothelial cell migration / detection of bacterium / T cell receptor binding / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / Signaling by FGFR4 in disease / energy homeostasis / GPVI-mediated activation cascade / positive regulation of lamellipodium assembly / cardiac muscle contraction / Signaling by FLT3 ITD and TKD mutants / Signaling by FGFR3 in disease / Tie2 Signaling / response to muscle stretch / Signaling by FGFR2 in disease / RAC1 GTPase cycle / Signaling by FLT3 fusion proteins / FLT3 Signaling / Signaling by FGFR1 in disease / positive regulation of smooth muscle cell proliferation
Similarity search - Function
PI3Kalpha, catalytic domain / PI3-kinase family, p85-binding domain / PI3-kinase family, p85-binding domain / Phosphatidylinositol 3-kinase, adaptor-binding domain / Phosphatidylinositol 3-kinase adaptor-binding (PI3K ABD) domain profile. / PI3-kinase family, Ras-binding domain / Phosphatidylinositol 3-kinase Ras-binding (PI3K RBD) domain / PI3-kinase family, ras-binding domain / Phosphatidylinositol 3-kinase Ras-binding (PI3K RBD) domain profile. / C2 phosphatidylinositol 3-kinase-type domain ...PI3Kalpha, catalytic domain / PI3-kinase family, p85-binding domain / PI3-kinase family, p85-binding domain / Phosphatidylinositol 3-kinase, adaptor-binding domain / Phosphatidylinositol 3-kinase adaptor-binding (PI3K ABD) domain profile. / PI3-kinase family, Ras-binding domain / Phosphatidylinositol 3-kinase Ras-binding (PI3K RBD) domain / PI3-kinase family, ras-binding domain / Phosphatidylinositol 3-kinase Ras-binding (PI3K RBD) domain profile. / C2 phosphatidylinositol 3-kinase-type domain / Phosphoinositide 3-kinase C2 / C2 phosphatidylinositol 3-kinase (PI3K)-type domain profile. / Phosphoinositide 3-kinase, region postulated to contain C2 domain / Phosphoinositide 3-kinase family, accessory domain (PIK domain) / Phosphoinositide 3-kinase family, accessory domain (PIK domain) / Phosphoinositide 3-kinase, accessory (PIK) domain superfamily / Phosphoinositide 3-kinase, accessory (PIK) domain / Phosphatidylinositol kinase / PIK helical domain profile. / Phosphatidylinositol 3- and 4-kinases signature 1. / Phosphatidylinositol 3/4-kinase, conserved site / Phosphatidylinositol 3- and 4-kinases signature 2. / Phosphatidylinositol 3-/4-kinase, catalytic domain superfamily / Phosphoinositide 3-kinase, catalytic domain / Phosphatidylinositol 3- and 4-kinase / Phosphatidylinositol 3- and 4-kinases catalytic domain profile. / Phosphatidylinositol 3-/4-kinase, catalytic domain / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / C2 domain superfamily / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / : / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Armadillo-type fold / Ubiquitin-like domain superfamily / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Protein kinase-like domain superfamily / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / HLA class I histocompatibility antigen, A alpha chain / Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.11 Å
AuthorsMa, J. / Baker, B.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI129543 United States
CitationJournal: Nat Med / Year: 2022
Title: Immunogenicity and therapeutic targeting of a public neoantigen derived from mutated PIK3CA.
Authors: Chandran, S.S. / Ma, J. / Klatt, M.G. / Dundar, F. / Bandlamudi, C. / Razavi, P. / Wen, H.Y. / Weigelt, B. / Zumbo, P. / Fu, S.N. / Banks, L.B. / Yi, F. / Vercher, E. / Etxeberria, I. / ...Authors: Chandran, S.S. / Ma, J. / Klatt, M.G. / Dundar, F. / Bandlamudi, C. / Razavi, P. / Wen, H.Y. / Weigelt, B. / Zumbo, P. / Fu, S.N. / Banks, L.B. / Yi, F. / Vercher, E. / Etxeberria, I. / Bestman, W.D. / Da Cruz Paula, A. / Aricescu, I.S. / Drilon, A. / Betel, D. / Scheinberg, D.A. / Baker, B.M. / Klebanoff, C.A.
History
DepositionDec 14, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2022Provider: repository / Type: Initial release
Revision 1.1May 11, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2May 25, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Oct 16, 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: HLA class I histocompatibility antigen, A alpha chain
B: Beta-2-microglobulin
C: Mutant PIK3CA peptide
D: T cell receptor, alpha chain
E: T cell receptor, beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,0007
Polymers94,8495
Non-polymers1512
Water00
1
D: T cell receptor, alpha chain
E: T cell receptor, beta chain
hetero molecules

A: HLA class I histocompatibility antigen, A alpha chain
B: Beta-2-microglobulin
C: Mutant PIK3CA peptide


Theoretical massNumber of molelcules
Total (without water)95,0007
Polymers94,8495
Non-polymers1512
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area10910 Å2
ΔGint-38 kcal/mol
Surface area38840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.282, 72.282, 475.730
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein HLA class I histocompatibility antigen, A alpha chain / Human leukocyte antigen A / HLA-A


Mass: 31628.838 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A, HLAA / Production host: Escherichia coli (E. coli) / References: UniProt: P04439
#2: Protein Beta-2-microglobulin


Mass: 11879.356 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Production host: Escherichia coli (E. coli) / References: UniProt: P61769

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Protein/peptide , 1 types, 1 molecules C

#3: Protein/peptide Mutant PIK3CA peptide / Phosphatidylinositol 4 / 5-bisphosphate 3-kinase catalytic subunit alpha isoform / PtdIns-3-kinase ...Phosphatidylinositol 4 / 5-bisphosphate 3-kinase catalytic subunit alpha isoform / PtdIns-3-kinase subunit alpha / Phosphatidylinositol 4 / 5-bisphosphate 3-kinase 110 kDa catalytic subunit alpha / p110alpha / Phosphoinositide-3-kinase catalytic alpha polypeptide / Serine/threonine protein kinase PIK3CA


Mass: 972.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P42336

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T cell receptor, ... , 2 types, 2 molecules DE

#4: Protein T cell receptor, alpha chain


Mass: 22681.869 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#5: Protein T cell receptor, beta chain


Mass: 27686.744 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)

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Non-polymers , 2 types, 2 molecules

#6: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION

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Details

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: 3.28 Å3/Da / Density % sol: 62.52 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop
Details: 10% w/v Polyethylene glycol 8,000, 200mM Magnesium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.11→50 Å / Num. obs: 24158 / % possible obs: 99.7 % / Redundancy: 20.2 % / Biso Wilson estimate: 84.91 Å2 / Rmerge(I) obs: 0.145 / Rpim(I) all: 0.032 / Rrim(I) all: 0.148 / Net I/σ(I): 25
Reflection shellResolution: 3.11→3.15 Å / Redundancy: 14.1 % / Rmerge(I) obs: 1.365 / Num. unique obs: 914 / CC1/2: 0.797 / Rpim(I) all: 0.335 / Rrim(I) all: 1.41 / % possible all: 97.6

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2XPG, 3QH3, 4PRH

2xpg

3qh3

4prh


Resolution: 3.11→49.51 Å / SU ML: 0.3871 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 24.9911
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2497 1903 8.31 %
Rwork0.1979 21008 -
obs0.2021 22911 95.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 98.42 Å2
Refinement stepCycle: LAST / Resolution: 3.11→49.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6502 0 10 0 6512
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026670
X-RAY DIFFRACTIONf_angle_d0.49399054
X-RAY DIFFRACTIONf_chiral_restr0.0392955
X-RAY DIFFRACTIONf_plane_restr0.00331196
X-RAY DIFFRACTIONf_dihedral_angle_d18.00652427
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.11-3.190.34011020.33271227X-RAY DIFFRACTION80.06
3.19-3.270.34231270.28831323X-RAY DIFFRACTION86.26
3.27-3.370.36241290.25811372X-RAY DIFFRACTION90.8
3.37-3.480.29071250.2371430X-RAY DIFFRACTION91.79
3.48-3.60.25371330.23161464X-RAY DIFFRACTION94.89
3.6-3.740.31681360.23181472X-RAY DIFFRACTION95.89
3.74-3.910.32771380.22091498X-RAY DIFFRACTION97.32
3.92-4.120.25111400.18831539X-RAY DIFFRACTION98.36
4.12-4.380.25721410.16911550X-RAY DIFFRACTION99.35
4.38-4.720.19771420.15251580X-RAY DIFFRACTION99.6
4.72-5.190.20211440.15881601X-RAY DIFFRACTION99.6
5.19-5.940.22831460.18091595X-RAY DIFFRACTION99.71
5.94-7.480.2641440.21451624X-RAY DIFFRACTION99.21
7.48-49.510.2181560.19111733X-RAY DIFFRACTION96.67
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)
15.07000702862-1.32370911920.4494958653894.76027389389-0.1522112134654.45889580620.005038689020770.01328082136780.0443320901128-0.1043870906950.00329785384870.0397922925943-0.2822842504090.0831848039554-0.002290476901780.376406410522-0.0661751672196-0.1530081880230.5297087786240.02599947225190.46594516218535.4931543998-31.4342845703-39.1685273025
27.28188114208-1.215937927810.06311370749535.306927948471.888330955624.57862968192-0.1894864467050.120425538844-0.533114096937-0.04065849054620.2560020841930.702732208750.378726314698-0.636706331966-0.09993831242290.830271433404-0.10234676969-0.3250919023080.701765769410.2785718548861.079690000736.01243984088-22.7865378002-56.9340851007
33.91851706643-1.847744264651.11164226497.40038966045-2.695309699827.417812583980.3398249647841.147516909130.550864603852-1.06907574601-0.34458548993-0.181584410104-0.002050170787150.375832272308-0.01750355123490.7766415572460.0379088462451-0.2357058575190.8572619843220.1441063808270.71748926219427.1888621267-24.627871555-63.9954277261
49.900738374711.661545214590.5047561774054.06029936830.9302522062244.413272528810.568136786875-0.571031765246-0.1312972386670.972653104593-0.6212760553260.5198195217260.6262912198660.109349962012-0.07093728930730.454800662753-0.105115979143-0.07969846371670.897423313855-0.1229284461530.6027625780440.3462078006-35.582280596-34.3151367387
56.93511019829-1.25271112523-2.046947100992.94259319321-1.211104622276.70692901794-0.455956002576-0.4239281354740.1056305343640.363210362810.1350122680980.0040173594319-0.407501522297-0.3409038888120.3102253834590.5987099557840.184638286954-0.1453906049330.685908267416-0.1281961968670.632049752013-24.5730401978-32.7050715283-10.4825008897
65.4844722282-0.1318763209922.797736017483.344839109110.3243844780884.096074306340.01850707235840.32702233431-0.0252673535987-0.0382170235759-0.0440367270307-0.321134290981-0.04881102456270.808894833434-0.08190325722740.3393734116110.00998154989702-0.1185300065050.9350169970380.05080680353570.681183162714-9.51160977312-34.122146584-27.9400895751
78.69282134871-1.49063031202-3.304008710346.64432212317-1.519301044933.82728572632-0.240246727089-1.32715937205-0.04672227664681.332178221770.561826723574-0.147029525442-0.4283614733470.571734033508-0.2891862305110.9658360529110.180771199616-0.1460475440981.5521272476-0.1154239136020.6049878328490.338118783985-36.940465247412.6522762995
83.316873656560.343353577731-0.7842529640744.11208681659-0.5807142673585.62863737322-0.390468260721-0.136741699639-0.1201572913730.3505764419250.310564390970.003235703183970.4605411100260.6136360197930.1303612325820.5951266984230.205678884391-0.1339539284741.460461943880.1650231586330.9473185170897.34075229808-43.1402510884-2.45350945373
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 180 )
2X-RAY DIFFRACTION2chain 'A' and (resid 181 through 274 )
3X-RAY DIFFRACTION3chain 'B' and (resid 1 through 99 )
4X-RAY DIFFRACTION4chain 'C' and (resid 1 through 9 )
5X-RAY DIFFRACTION5chain 'D' and (resid 8 through 112 )
6X-RAY DIFFRACTION6chain 'E' and (resid 3 through 119 )
7X-RAY DIFFRACTION7chain 'D' and (resid 113 through 198)
8X-RAY DIFFRACTION8chain 'E' and (resid 120 through 249)

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