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- PDB-7s2s: nanobody bound to Interleukin-2Rbeta -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 7s2s
Titlenanobody bound to Interleukin-2Rbeta
Components
  • IL2Rb-binding nanobody
  • Interleukin-2 receptor subunit betaIL-2 receptor
KeywordsPROTEIN BINDING / nanobody / cytokine receptor
Function / homology
Function and homology information


interleukin-2 receptor complex / interleukin-2 receptor activity / interleukin-15 receptor activity / interleukin-2 binding / interleukin-2-mediated signaling pathway / interleukin-15-mediated signaling pathway / Interleukin-15 signaling / Interleukin-2 signaling / cytokine receptor activity / immunoglobulin mediated immune response ...interleukin-2 receptor complex / interleukin-2 receptor activity / interleukin-15 receptor activity / interleukin-2 binding / interleukin-2-mediated signaling pathway / interleukin-15-mediated signaling pathway / Interleukin-15 signaling / Interleukin-2 signaling / cytokine receptor activity / immunoglobulin mediated immune response / Interleukin receptor SHC signaling / coreceptor activity / positive regulation of phagocytosis / cytokine-mediated signaling pathway / RAF/MAP kinase cascade / protein-containing complex assembly / endosome / external side of plasma membrane / negative regulation of apoptotic process / cell surface / signal transduction / membrane / plasma membrane / cytosol
Similarity search - Function
Interleukin-2 receptor subunit beta, N-terminal / Interleukin-2 receptor subunit beta N-terminal domain 1 / Short hematopoietin receptor family 1 signature. / Short hematopoietin receptor, family 1, conserved site / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Interleukin-2 receptor subunit beta
Similarity search - Component
Biological speciesCamelus bactrianus (Bactrian camel)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.93 Å
AuthorsGlassman, C.R. / Jude, K.M. / Yen, M. / Garcia, K.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R37-AI051321 United States
CitationJournal: Cell / Year: 2022
Title: Facile discovery of surrogate cytokine agonists.
Authors: Yen, M. / Ren, J. / Liu, Q. / Glassman, C.R. / Sheahan, T.P. / Picton, L.K. / Moreira, F.R. / Rustagi, A. / Jude, K.M. / Zhao, X. / Blish, C.A. / Baric, R.S. / Su, L.L. / Garcia, K.C.
History
DepositionSep 3, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 6, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Apr 27, 2022Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.3Oct 18, 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
C: IL2Rb-binding nanobody
B: Interleukin-2 receptor subunit beta
A: IL2Rb-binding nanobody
D: Interleukin-2 receptor subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,26623
Polymers83,5624
Non-polymers4,70419
Water3,477193
1
C: IL2Rb-binding nanobody
B: Interleukin-2 receptor subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,8939
Polymers41,7812
Non-polymers2,1127
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: IL2Rb-binding nanobody
D: Interleukin-2 receptor subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,37314
Polymers41,7812
Non-polymers2,59212
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.698, 69.505, 91.721
Angle α, β, γ (deg.)99.566, 99.854, 90.191
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

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Antibody / Protein , 2 types, 4 molecules CABD

#1: Antibody IL2Rb-binding nanobody


Mass: 16581.367 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Camelus bactrianus (Bactrian camel) / Cell line (production host): HEK 293F / Production host: Homo sapiens (human)
#2: Protein Interleukin-2 receptor subunit beta / IL-2 receptor / IL-2 receptor subunit beta / IL-2R subunit beta / IL-2RB / High affinity IL-2 receptor subunit beta ...IL-2 receptor subunit beta / IL-2R subunit beta / IL-2RB / High affinity IL-2 receptor subunit beta / Interleukin-15 receptor subunit beta / p70-75 / p75


Mass: 25199.594 Da / Num. of mol.: 2 / Fragment: extracellular domain
Source method: isolated from a genetically manipulated source
Details: protein was methylated before crystallization / Source: (gene. exp.) Homo sapiens (human) / Gene: IL2RB, IL15RB / Cell line (production host): HEK 293F / Production host: Homo sapiens (human) / References: UniProt: P14784

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Sugars , 2 types, 6 molecules

#3: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#4: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE

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Non-polymers , 2 types, 206 molecules

#5: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 193 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.17 Å3/Da / Density % sol: 61.19 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 5.5
Details: 0.23 M ammonium sulfate, 0.08 M Bis Tris pH 5.5, 23% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 6, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.92→44.53 Å / Num. obs: 73848 / % possible obs: 94.5 % / Redundancy: 3.6 % / CC1/2: 0.996 / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.062 / Rrim(I) all: 0.119 / Net I/σ(I): 7.8 / Num. measured all: 263682
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.92-1.973.41.3581426542280.5560.8481.6060.973
8.59-44.533.50.03230188570.9980.020.0382999.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.19.2refinement
XDSdata reduction
Aimless0.7.7data scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2b5i, 5lhr

2b5i

5lhr


Resolution: 1.93→44.53 Å / SU ML: 0.2789 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 29.2824
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2471 2007 2.73 %
Rwork0.2127 71626 -
obs0.2137 73633 95.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 54.65 Å2
Refinement stepCycle: LAST / Resolution: 1.93→44.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5163 0 295 193 5651
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045589
X-RAY DIFFRACTIONf_angle_d0.70337618
X-RAY DIFFRACTIONf_chiral_restr0.0457872
X-RAY DIFFRACTIONf_plane_restr0.0052939
X-RAY DIFFRACTIONf_dihedral_angle_d15.17262034
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.93-1.980.37651310.35494836X-RAY DIFFRACTION92.03
1.98-2.030.34451430.32835201X-RAY DIFFRACTION95.39
2.03-2.090.37251360.30685035X-RAY DIFFRACTION95.88
2.09-2.160.31351480.27985091X-RAY DIFFRACTION95.52
2.16-2.240.33751500.27545178X-RAY DIFFRACTION95.88
2.24-2.330.27271410.24655073X-RAY DIFFRACTION96
2.33-2.430.29661520.24895105X-RAY DIFFRACTION96.05
2.43-2.560.28491320.25325176X-RAY DIFFRACTION96.21
2.56-2.720.26291440.23795112X-RAY DIFFRACTION96.23
2.72-2.930.32331500.2325136X-RAY DIFFRACTION96.6
2.93-3.230.25381410.22055176X-RAY DIFFRACTION96.57
3.23-3.690.22251460.18415171X-RAY DIFFRACTION96.92
3.69-4.650.17021470.1585174X-RAY DIFFRACTION96.83
4.65-44.530.20881460.17595162X-RAY DIFFRACTION96.93
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)
10.2336312177170.325122183084-0.3543707167231.22623277527-0.1726800273941.4224719069-0.158404965983-0.4551786226150.06247255245931.071773721470.147817863839-0.0850007320166-0.1614755614940.06078780021260.007020875920851.141056807980.06648902057580.1604707620440.690973718233-0.1442122369540.4584924184391.9540825508747.737480867.32394795555
21.772794373160.382479423256-0.5061859686092.9098545184-0.9939993303672.49253592493-0.0599754248631-0.1957522285810.05554599412281.009496314840.1038461898580.7852352779070.603134214391-0.366123007888-0.05678479979420.811722911263-0.03645358168320.1641905825080.48328899175-0.0584610510160.400437925497-3.4223006491442.5653848521-1.07459034735
31.724868735270.0523207818819-1.724215949011.84904764367-0.7237468789821.981320920560.0326684156097-0.535267010898-0.06413829915190.919607346351-0.08020683529121.04468676846-0.0530871041609-1.00367790703-0.08817148717630.7231134054920.06075436841460.3010992024280.69163782275-0.1012189579430.670695045685-9.7740665485650.1468694353-0.83394527007
40.820360112682-0.689960868736-0.5294082827033.21672331827-0.479422857691.886798241150.0826894130127-0.4607654821440.1064679823761.364112551380.08815720070010.828121042019-0.27584777682-0.17915664782-0.044696007411.16550066394-0.02282490856730.2101693976480.682838388057-0.1576126001860.381679124433-4.4775621939450.35404127246.65982395932
51.835305062850.0986289461511-0.5426116411192.84312213534-0.1688357152121.32537092541-0.05298063306-0.33532350465-0.01184544115991.083003456890.1097937584920.1268371295010.21800548356-0.322112925651-0.03813535794950.5663221205510.01283020404880.08272917141550.385618431871-0.03097944507110.3658084979480.58823108910242.0222792866-5.36952445632
62.696042029940.117880605636-0.01777525292992.98432103716-0.46175625611.902651316110.0426474842914-0.418577630277-0.3132616330361.208164990570.164600177893-0.04920794134940.3292596700130.6219202164450.0144043171850.8959076746630.086102377291-0.0912437487620.5063985083710.05523703883150.3224204705434.3507897477737.11119735030.712920218562
70.154784748416-0.18922469578-0.06858798120091.48113151872-0.04913835845760.0996122631160.0622837141886-0.469822491680.2071729509210.9011948641250.08038970417680.96702851901-0.180386867068-0.162822198093-0.005147453561241.27521730701-0.02628806089480.3911511873771.114679635250.2359323706140.720516895885-11.895929752542.142497175114.4411019205
82.324538188480.4873048550260.3851928198873.284287934930.3774568313312.460747893840.089288849551-0.0844143441422-0.1026476312470.2062998569950.01392841718980.2576933012270.194629728678-0.0839116066221-0.02861633736680.1993194205380.0130895104484-0.02827265203840.2385537312290.009411947761570.3631813708271.6670937270534.5696031803-23.1432437434
91.3848240193-0.764648094603-0.7678018993441.542524890710.653549429690.8912503871490.005020504327730.003395075921490.0363904116887-0.116342932802-0.00152476615632-0.340926544502-0.01627887404660.04681813564510.0301298849940.216059017112-0.013355261773-0.0132773089830.213609139833-0.000123156722410.39019065563525.161569888833.9044353742-32.9879723203
100.340844829298-0.0421214556430.08963446813651.8541070276-1.17751107811.03141942074-0.09577107503160.7606068887520.473236902398-1.304621630290.047702690992-0.3443225506590.03418380076430.0559289597219-0.2696758008731.610302154360.05254124585010.2687819575460.8714720586570.08219215350590.58433850589941.016866234380.0362119785-73.6906455619
110.1574668384810.3044926373620.09185578194450.967976317714-0.5138679873051.36560975712-0.1010577781820.3808981901480.300492432657-1.29974173362-0.276682348252-0.296301840631-0.478844858528-0.431639334534-0.2048854829231.235862704370.180723077785-0.002520417521890.6701881747290.04165301732890.4708987049231.671965115683.7545376068-64.5588867323
121.35895264094-0.285801991129-0.6273615586912.926202719271.072183479711.875395731830.04060843455240.1720326448520.112204831304-1.02014605660.0815980323588-0.671414845670.02217693015070.375480343475-0.02938145860620.8562796787580.04818794281720.2528886910080.504711253174-0.00334696923020.47148640104842.291063824476.6141168897-61.4111139467
132.8215604304-0.374283046946-1.83045777441.044802856320.4644177034391.45315537075-0.0947509870054-0.09236738773240.188990683597-0.8658925158060.0980530361158-0.821641684669-0.3863728407240.82503031774-0.09190763551210.989749701034-0.1839250002170.5409463680450.596208239153-0.0850324672330.70959072579247.801898482284.7142135109-60.9161802291
140.1936032884440.561249962010.2766462381753.71748988022-0.08130284228972.33529511954-0.1459000194370.2994297235020.394218434736-1.41225471481-0.0335588350887-0.236622984902-0.446127963027-0.542773730309-0.08045332428161.461804955350.1820313179130.2031064912280.6957981237930.1537629587040.46842575774935.312935062587.7754122742-67.8041196429
151.54244024576-0.7170617450010.4851794586661.50635165539-1.645652912862.11155400410.3766158560670.8388728545520.367716175696-1.312072000390.0954158299913-0.723658958455-0.1911587401170.0809658697557-0.08383354411131.393317229910.1860166523840.7193591734470.860660658699-0.01570425811831.1227362545653.890043862980.3847690911-69.803477984
161.219373622190.308840164008-0.6985197597472.235169116580.1744554521941.224130013790.3280256943150.3163274451080.27156469811-1.12848688089-0.079212363257-0.361855224071-0.218106048860.321395077042-0.03361688702170.5486642295920.04271574135990.08369173165950.390536359394-0.0003237401694480.3489062884736.786123232776.5349240887-56.5398596011
171.37813341035-0.349582119074-0.3853873608220.866782336431-0.1295976611982.238874098360.1004146253360.760098489302-0.0267970005954-1.308431681280.0828398941492-0.5958874551780.3442843250320.1902325152510.1078155448971.123701958460.05631913308820.2388613498560.68598061434-0.09734204973710.48481295212140.815509913573.7210052791-68.678288522
183.312985696930.178268165701-0.3351561963422.79006152124-0.3043071367562.12528239018-0.022143355010.366841100408-0.469830708214-0.3320222108810.0410746133329-0.2802539410170.414485628965-0.0854406725248-0.0001959762092160.285729814617-0.0364632121947-0.03138837745320.253749987106-0.02736466454830.37887966798833.403184429766.1628961573-42.0485768658
191.80163773073-0.2714978547730.07570646887243.41959392278-0.4042522182181.461526021830.0718429491643-0.13267554336-0.0370250452932-0.198621951662-0.0357441705235-0.174206653564-0.03512901029520.0227759059313-0.01576105851650.189617088937-0.00847205558484-0.03550473093210.230388863789-0.01740593062750.39101263780235.666559716271.4479821739-35.4059675116
204.893943895690.5763751513660.05602895440821.32298840628-1.411401417642.735503376830.2856841570370.290145543386-0.323614271214-0.600782315583-0.0892663670051-0.9816472131690.4018206519490.91031003251-0.03908558301420.3509776980440.1277184129820.06809195078670.423210899529-0.0344837425280.50561505879442.309715776766.3393827734-46.5124630447
212.526717323740.112055266893-0.06554934030114.63206479589-0.1341201212893.409820944330.06093405242680.242232693349-0.229143523793-0.5095610435450.0611474047132-0.9349392446880.3444062394450.482492190036-0.01424077916560.3760587065050.03632271911370.02844079672290.378340084805-0.04521199869430.51108195260639.861691907968.3206453544-48.6095094402
221.443865981671.21545288802-0.7034946558871.87858391818-1.01993490320.5226325624890.0568568113674-0.02587906535720.1503261693340.1934325366060.006700590229460.379889243535-0.060516543166-0.0244444178454-0.09790836449570.2203371781960.0001716484544110.0129765485890.227285965554-0.002577439482680.4290368115579.6967809252368.784973953-27.5317616552
239.21220087026-3.53809364816-7.324021195644.922340886028.096286390121.999964884450.0856905799158-0.210611491230.4330228666390.4603342028810.07347935281210.843063769688-0.41883692457-0.370573016306-0.2917637083770.330580882677-0.05782781315420.4235375666430.9024955241130.02459709647980.961504569646-12.082280998558.9062305996-13.5927289539
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'C' and (resid 3 through 31 )CA3 - 311 - 29
22chain 'C' and (resid 32 through 56 )CA32 - 5630 - 54
33chain 'C' and (resid 57 through 70 )CA57 - 7055 - 68
44chain 'C' and (resid 72 through 90 )CA72 - 9070 - 88
55chain 'C' and (resid 91 through 114 )CA91 - 11489 - 112
66chain 'C' and (resid 115 through 121 )CA115 - 121113 - 119
77chain 'C' and (resid 122 through 129 )CA122 - 129120 - 127
88chain 'B' and (resid 32 through 114 )BB32 - 1141 - 78
99chain 'B' and (resid 115 through 235 )BB115 - 23579 - 199
1010chain 'A' and (resid 2 through 17 )AL2 - 171 - 16
1111chain 'A' and (resid 18 through 33 )AL18 - 3317 - 32
1212chain 'A' and (resid 34 through 56 )AL34 - 5633 - 55
1313chain 'A' and (resid 57 through 70 )AL57 - 7056 - 69
1414chain 'A' and (resid 72 through 82 )AL72 - 8271 - 81
1515chain 'A' and (resid 83 through 90 )AL83 - 9082 - 89
1616chain 'A' and (resid 91 through 114 )AL91 - 11490 - 113
1717chain 'A' and (resid 115 through 128 )AL115 - 128114 - 127
1818chain 'D' and (resid 32 through 65 )DM32 - 651 - 34
1919chain 'D' and (resid 66 through 103 )DM66 - 10335 - 72
2020chain 'D' and (resid 104 through 114 )DM104 - 11473 - 83
2121chain 'D' and (resid 115 through 124 )DM115 - 12484 - 93
2222chain 'D' and (resid 125 through 233 )DM125 - 23394 - 202
2323chain 'D' and (resid 234 through 235 )DM234 - 235203 - 204

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