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- PDB-7ntk: PALS1 PDZ1 domain with SARS-CoV-2_E PBM complex -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 7ntk
TitlePALS1 PDZ1 domain with SARS-CoV-2_E PBM complex
Components
  • Envelope small membrane protein
  • MAGUK p55 subfamily member 5
KeywordsCELL ADHESION / cell polarity / PALS1 / SARS-CoV-2_E
Function / homology
Function and homology information


disruption of cellular anatomical structure in another organism / protein localization to myelin sheath abaxonal region / SARS-CoV-1 targets PDZ proteins in cell-cell junction / viral budding from Golgi membrane / establishment or maintenance of polarity of embryonic epithelium / myelin assembly / morphogenesis of an epithelial sheet / Tight junction interactions / SARS-CoV-2 targets PDZ proteins in cell-cell junction / regulation of transforming growth factor beta receptor signaling pathway ...disruption of cellular anatomical structure in another organism / protein localization to myelin sheath abaxonal region / SARS-CoV-1 targets PDZ proteins in cell-cell junction / viral budding from Golgi membrane / establishment or maintenance of polarity of embryonic epithelium / myelin assembly / morphogenesis of an epithelial sheet / Tight junction interactions / SARS-CoV-2 targets PDZ proteins in cell-cell junction / regulation of transforming growth factor beta receptor signaling pathway / cytoplasmic capsid assembly / myelin sheath adaxonal region / lateral loop / Regulation of gap junction activity / Schmidt-Lanterman incisure / establishment or maintenance of epithelial cell apical/basal polarity / peripheral nervous system myelin maintenance / apical junction complex / generation of neurons / central nervous system neuron development / endoplasmic reticulum-Golgi intermediate compartment / host cell Golgi membrane / monoatomic ion channel activity / bicellular tight junction / Maturation of protein E / endoplasmic reticulum-Golgi intermediate compartment membrane / protein localization to plasma membrane / adherens junction / cerebral cortex development / gene expression / perikaryon / Translation of Structural Proteins / Virion Assembly and Release / Induction of Cell-Cell Fusion / structural constituent of virion / Attachment and Entry / apical plasma membrane / protein domain specific binding / axon / apoptotic process / SARS-CoV-2 activates/modulates innate and adaptive immune responses / virion membrane / Golgi apparatus / protein-containing complex / extracellular exosome / ATP binding / identical protein binding / membrane / plasma membrane / cytoplasm
Similarity search - Function
L27-N / MPP5, SH3 domain / L27_N / Envelope small membrane protein, SARS-CoV-2-like / Envelope small membrane protein, coronavirus / Envelope small membrane protein, betacoronavirus / Coronavirus small envelope protein E / Coronavirus envelope (CoV E) protein profile. / L27 domain, C-terminal / L27 domain ...L27-N / MPP5, SH3 domain / L27_N / Envelope small membrane protein, SARS-CoV-2-like / Envelope small membrane protein, coronavirus / Envelope small membrane protein, betacoronavirus / Coronavirus small envelope protein E / Coronavirus envelope (CoV E) protein profile. / L27 domain, C-terminal / L27 domain / : / domain in receptor targeting proteins Lin-2 and Lin-7 / L27 domain / L27 domain profile. / L27 domain superfamily / Guanylate kinase, conserved site / Guanylate kinase-like signature. / Guanylate kinase-like domain profile. / Guanylate kinase-like domain / Variant SH3 domain / Guanylate kinase/L-type calcium channel beta subunit / Guanylate kinase / Guanylate kinase homologues. / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
CITRATE ANION / Envelope small membrane protein / Protein PALS1
Similarity search - Component
Biological speciesHomo sapiens (human)
Severe acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsJavorsky, A. / Kvansakul, M.
CitationJournal: Commun Biol / Year: 2021
Title: Structural basis of coronavirus E protein interactions with human PALS1 PDZ domain.
Authors: Javorsky, A. / Humbert, P.O. / Kvansakul, M.
History
DepositionMar 10, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 16, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 21, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MAGUK p55 subfamily member 5
B: MAGUK p55 subfamily member 5
C: Envelope small membrane protein
D: MAGUK p55 subfamily member 5
E: Envelope small membrane protein
F: MAGUK p55 subfamily member 5
G: Envelope small membrane protein
H: Envelope small membrane protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,66314
Polymers41,1638
Non-polymers4996
Water6,467359
1
A: MAGUK p55 subfamily member 5
C: Envelope small membrane protein


Theoretical massNumber of molelcules
Total (without water)10,2912
Polymers10,2912
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1100 Å2
ΔGint-6 kcal/mol
Surface area5150 Å2
MethodPISA
2
B: MAGUK p55 subfamily member 5
G: Envelope small membrane protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,6666
Polymers10,2912
Non-polymers3754
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1180 Å2
ΔGint-8 kcal/mol
Surface area5630 Å2
MethodPISA
3
D: MAGUK p55 subfamily member 5
E: Envelope small membrane protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,3533
Polymers10,2912
Non-polymers621
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1190 Å2
ΔGint-2 kcal/mol
Surface area5330 Å2
MethodPISA
4
F: MAGUK p55 subfamily member 5
H: Envelope small membrane protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,3533
Polymers10,2912
Non-polymers621
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area910 Å2
ΔGint-8 kcal/mol
Surface area5540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)28.688, 103.762, 59.076
Angle α, β, γ (deg.)90.000, 103.979, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
MAGUK p55 subfamily member 5


Mass: 9391.783 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: At the n-terminal of chain A,B,D,F, sequence GPLGS is part of the expression tag
Source: (gene. exp.) Homo sapiens (human) / Gene: MPP5, PALS1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Codon+ / References: UniProt: Q8N3R9
#2: Protein/peptide
Envelope small membrane protein / E / sM protein


Mass: 899.067 Da / Num. of mol.: 4 / Source method: obtained synthetically
Source: (synth.) Severe acute respiratory syndrome coronavirus 2
References: UniProt: P0DTC4
#3: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 359 / Source method: isolated from a natural source / Formula: H2O
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: 2.07 Å3/Da / Density % sol: 40.66 % / Description: plate
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2M Sodium acetate trihydrate, 0.1M TRIS pH 8.5, 30% w/v PEG 4000
PH range: 7.2-8.5 / Temp details: 293.15

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95372 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 9, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 1.9→34.59 Å / Num. obs: 26253 / % possible obs: 99.4 % / Redundancy: 2.9 % / Biso Wilson estimate: 21.91 Å2 / CC1/2: 0.987 / Rmerge(I) obs: 0.129 / Net I/σ(I): 3.4
Reflection shellResolution: 1.9→1.94 Å / Rmerge(I) obs: 0.725 / Num. unique obs: 4885 / CC1/2: 0.431

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874+SVNrefinement
DIALSdata reduction
Aimlessdata scaling
PHASER1.15.2-3472-000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4UU6

4uu6


Resolution: 1.9→29.61 Å / SU ML: 0.2398 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 22.9017
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2287 1316 5.03 %
Rwork0.1957 24844 -
obs0.1975 26160 99.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.31 Å2
Refinement stepCycle: LAST / Resolution: 1.9→29.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2753 0 33 359 3145
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00552816
X-RAY DIFFRACTIONf_angle_d0.58143800
X-RAY DIFFRACTIONf_chiral_restr0.0538468
X-RAY DIFFRACTIONf_plane_restr0.0039493
X-RAY DIFFRACTIONf_dihedral_angle_d21.85861059
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.980.31151600.28262711X-RAY DIFFRACTION98.69
1.98-2.070.24741220.23012764X-RAY DIFFRACTION98.36
2.07-2.180.25781230.21842778X-RAY DIFFRACTION99.18
2.18-2.310.24621350.20542747X-RAY DIFFRACTION99.17
2.31-2.490.25551560.20522753X-RAY DIFFRACTION99.28
2.49-2.740.23661370.21442764X-RAY DIFFRACTION99.21
2.74-3.140.21541590.19782786X-RAY DIFFRACTION99.29
3.14-3.950.19951650.16892755X-RAY DIFFRACTION99.62
3.95-29.610.2211590.17292786X-RAY DIFFRACTION99.16
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)
12.27730525179-1.18126848027-2.030202434741.274789942612.174558566469.231785979890.0610558196027-0.05203275759-0.0777703641055-0.1658664746-0.05969746808040.104574463396-0.08145669968560.04143646410830.07411903412080.1578773905030.02672625197910.00555631283780.145777320675-0.004168252449180.197517965178-15.579357548747.26410709762.21536907679
23.405840667441.509098361850.8543375175946.775635510131.812737454463.099486110310.2050401939130.191565278158-0.0100057549514-0.290404520513-0.312239577692-0.107525191958-0.2164399358190.2612506615180.220660460060.2714090677360.0823624189471-0.007121039801680.220413048040.003604813505480.191490904406-5.9718745803344.2142852816-12.1196403175
32.23548373767-0.7784472942391.100109298162.31858601895-0.201197346725.186519930260.0981712301583-0.03521612064350.385229198189-0.128168914659-0.104296037974-0.140672458172-0.200931599684-0.04939742372370.04576339454930.185596593464-0.0007467721568470.03668289326630.187903784373-0.006695695427120.26954840307-6.2550520647154.8185744806-0.682351636478
43.836142503440.9801638129550.9711344892713.167665687310.3580313410181.202650200910.253911928706-0.193689263389-0.2783812493430.295124493172-0.178678465897-0.1048875005590.1743174903850.193824156957-0.110784811110.160506864996-0.01563557667340.008110035971550.1579584136340.007591197138570.149411014581-5.9552193076244.05211527096.32212140385
54.176267364932.498509498615.088360593921.488115098743.037706604886.998232525980.3282210609570.463407895051-0.4136151586810.0383977297965-0.0942841642957-0.2304612967970.5450505782460.0613426281939-0.2415040434960.2064241295020.0003166647954590.04230303404320.213155252484-0.03571316897930.2997908570940.55573574528242.5620524015-2.35719065323
63.84073345963-1.03933069419-0.6861351198341.741765217031.312486652174.440189053540.02200770069330.2224438241-0.131331463949-0.0429827240894-0.2248199509370.1752779438690.310480476155-0.2172431316190.07967793735610.182607616136-0.02476206377690.01607626773250.196016411032-0.0106028429970.156896594029-11.995400277846.0008711359-0.126719348977
70.7139062037250.635827085340.936278688350.7881648534221.18688331835.52803180956-0.0384273216924-0.0445348556273-0.2049166625480.0324814534873-0.157469245922-0.00978837243692-0.130818851186-0.410601935520.1519179433540.2045792092140.0224987290352-0.009645205843890.305575206585-0.01525425697960.217393375735-13.728627100126.2142161371-2.23702430127
82.2205330671-1.21560306141-1.087739044322.045691190981.689111524354.752458125650.0331261503297-0.0395008458898-0.06707856228610.1954988120070.141766204294-0.1537735962950.170045374332-0.0261816426991-0.05372905828380.138939345535-0.0259400630984-0.04128439333090.168659459919-0.0006465961904970.151581111972-0.87895495725822.18070212040.727655673132
98.37088359511-3.800057618383.652383204175.807705018790.6662261009552.916340655760.0637112601497-1.042653325730.2516747493630.585225700748-0.1206384563440.460879726680.417524395322-0.5271585615810.02646004958740.169548162596-0.0328515458690.04065459948610.3232203841860.08157536454750.291485165402-9.0456473269117.21591798219.64347152564
104.34383795993-1.65994741098-4.497708877294.462259240393.786020855265.77003258981-0.1874408886750.032241159384-0.6491767050120.896094954917-0.02340909915570.3497816691711.08588931427-0.7075376909660.09220600300310.237661603668-0.0791137516787-0.03248562084580.2706248096630.08511095738080.314259482131-9.4984223370317.0436200988-0.597676424242
111.82150728298-0.7342102282170.225444657220.419054616562-0.5850894760941.55793436343-0.0696912135499-0.03436619432590.1050704296590.04266710484350.0378823086367-0.000817622634739-0.274699226440.05182764149650.0221321644750.1924365682450.0012115795446-0.01501421177990.173237812024-0.01842429911960.200574393869-4.1444233589129.7183842217-1.50975300068
120.7950437338910.678108650630.4290841136173.530549858345.14925704417.99900801373-0.02796786662190.617369800121-0.6884576055930.1756370937330.097130520597-0.5118098062061.096075055820.5734526557010.07381123206010.2589516401770.0262107558709-0.02808423908380.311576318257-0.06505519641110.402576775621-11.539284351341.796276198732.1793533234
138.996902985072.847076288643.22839419281.468039255360.5244938277561.599455304090.432889105127-0.9898107308141.00216640757-0.069590908457-0.945452495181-0.604520118714-0.5153741308560.216896103290.4783447087690.3394375725250.02999389970.1227936964370.4980983091710.107673374890.4772769565313.3808619200353.1136009474-1.5354565625
141.560475573850.0455546511406-0.8903549486211.17917407702-0.01597269134152.06707311966-0.00542574234543-0.0161301778423-0.150157427951-0.08642402769940.1853047276560.01959736602260.482880172133-0.0163503462011-0.09371292192630.271277333558-0.0467335217357-0.005934845714240.225862317284-0.001750797661280.237368676306-5.8828808297516.710281542832.546858174
152.54088269715-0.2800443506461.353950826110.796933602152-0.1495063995183.89004098461-0.02779430579640.0249523182240.1469595111640.1254953491250.0554310826796-0.176690551591-0.008877423445610.07502515844660.03063848800260.20513958985-0.0324289937727-0.01260449739390.1722631525810.01722623456290.1881606309151.6449992155827.292564602926.7709498782
166.21989948792.41705298008-1.258360186674.35250985981-4.036069792413.940561247310.002894459018250.6744478623410.230002768857-0.07018554900490.2931748810380.675716308901-0.366985638732-1.26356958071-0.3685201157340.1716196944830.0354706464276-0.01588665651410.3331788268490.0008607824992430.17951429596-10.004461333527.657536468720.0083276161
173.504364640080.455239418383-0.3266226813951.5106015785-0.8033883799010.5653099195-0.1166279318290.0614450914672-0.1052947859490.02364069843860.11725761919-0.0342741667570.00543117371411-0.1005008194710.0009130296258180.16834268662-0.01564605829330.008887412434170.1650223322970.00363767637670.15226360021.4364637905720.498277943929.3106644406
184.911262328086.18558142002-1.630459596277.78367745763-2.053066736790.5452091671380.5596906362460.1063460729290.5670075742510.86313990582-0.35293761035-0.226022497793-0.327806239230.0597226289296-0.1399757251420.3042444347370.0131696135089-0.01726452799330.294323589978-0.05141689297910.3133275124065.6408102172831.574571219723.927370766
192.06251709099-0.1587566241651.298828448531.60349843387-0.8342762353462.042953355620.0309162741188-0.1148574263150.2351844709190.261156278186-0.09599469425350.166017179165-0.0528026237679-0.1706509753460.0483274841040.2892026899150.03241985253880.009742508378760.220347590851-0.03705542977340.244816595378-21.690874454456.6844138124.8657069674
204.06989725032-0.0673343140551-0.8111862852732.02526134293-0.6688281709213.566127463210.02305544100240.148108219941-0.0556199408813-0.174318013319-0.2143098021190.0355313999315-0.45022059843-0.2554630017780.1995788747460.257489738874-0.0347742356247-0.03027253694440.1826922345040.01259558270280.174628869406-13.424469612447.077725982331.2091813312
216.01974786581.39481370939-2.067567284492.63740654395-0.6695343906024.278904117520.1680064430930.158003559936-0.1208201946870.127457437838-0.1071488751970.166578707565-0.226815583837-0.1993693464680.2485008901820.2467850087890.006167598880090.003017652847980.158935350135-0.04850122537640.203306891697-16.734847944943.032971997127.2145767392
225.16435234353-1.687709499611.949236496432.58828471646-4.559545907158.294105576710.199672258307-0.516984323172-0.4411441094370.5680595048570.08746564110990.150105282631-0.198631015912-0.290905895192-0.2799346335390.2424965972150.00229989941384-0.03853739456330.2899465356080.03150080550450.159937815359-26.07188008145.565903362336.4322234636
232.559218012120.2821007071060.467495988241.67051394423-0.07072573427391.02007841998-0.16759459375-0.1505341905270.169533058787-0.2082463560360.1495882825730.1169426603090.02439571254790.0401339407483-0.009975004009530.1914866548140.021499465308-0.01110794439760.1482977529570.0008698495273630.169663630919-14.883749833951.588217715424.3640971727
242.93722972043-0.6347205583880.8202776564591.42673783164-1.106542023181.8341025724-0.062715023052-0.4001079178660.07095198347470.1352285093670.05704290219580.0968902225866-0.124716375166-0.2865031588410.0343791913080.2393059342840.0561137284269-0.01129774853040.19710367792-0.02144080760680.200973070305-13.113589294554.004779635430.6693038083
256.46330050405-7.10506435268-3.107587198688.368635874365.441572672478.82722124191.129518333631.2617042755-0.851011105154-0.576713035307-0.557317012694-0.438904593194-0.1126169122960.3762196868570.1108785996510.382502847092-0.00243355660297-0.05473174678290.446230187383-0.1423249162750.3769046828056.3065864591519.4396547389-0.0119021042016
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 250 through 261 )AA250 - 2611 - 12
22chain 'A' and (resid 262 through 268 )AA262 - 26813 - 19
33chain 'A' and (resid 269 through 299 )AA269 - 29920 - 50
44chain 'A' and (resid 300 through 313 )AA300 - 31351 - 64
55chain 'A' and (resid 314 through 323 )AA314 - 32365 - 74
66chain 'A' and (resid 324 through 335 )AA324 - 33575 - 86
77chain 'B' and (resid 250 through 261 )BC250 - 2611 - 12
88chain 'B' and (resid 262 through 283 )BC262 - 28313 - 34
99chain 'B' and (resid 284 through 292 )BC284 - 29235 - 43
1010chain 'B' and (resid 293 through 299 )BC293 - 29944 - 50
1111chain 'B' and (resid 300 through 334 )BC300 - 33451 - 85
1212chain 'H' and (resid 206 through 211 )HN206 - 2111 - 6
1313chain 'C' and (resid 205 through 211 )CH205 - 2111 - 7
1414chain 'D' and (resid 250 through 261 )DI250 - 2611 - 12
1515chain 'D' and (resid 262 through 283 )DI262 - 28313 - 34
1616chain 'D' and (resid 284 through 291 )DI284 - 29135 - 42
1717chain 'D' and (resid 292 through 335 )DI292 - 33543 - 88
1818chain 'E' and (resid 205 through 211 )EK205 - 2111 - 7
1919chain 'F' and (resid 250 through 261 )FL250 - 2611 - 12
2020chain 'F' and (resid 262 through 276 )FL262 - 27613 - 27
2121chain 'F' and (resid 277 through 283 )FL277 - 28328 - 34
2222chain 'F' and (resid 284 through 292 )FL284 - 29235 - 43
2323chain 'F' and (resid 293 through 313 )FL293 - 31344 - 64
2424chain 'F' and (resid 314 through 335 )FL314 - 33565 - 88
2525chain 'G' and (resid 205 through 211 )GM205 - 2111 - 7

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