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- PDB-8phv: Structure of Human selenomethionylated Cdc123 bound to domain 3 o... -

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Basic information

Entry
Database: PDB / ID: 8phv
TitleStructure of Human selenomethionylated Cdc123 bound to domain 3 of eIF2 gamma
Components
  • Cell division cycle protein 123 homolog
  • Eukaryotic translation initiation factor 2 subunit 3
KeywordsTRANSLATION / eIF2 / translation initiation / chaperone / Cdc123 / ATP grasp
Function / homology
Function and homology information


eukaryotic translation initiation factor 2 complex assembly / Cellular response to mitochondrial stress / Response of EIF2AK1 (HRI) to heme deficiency / Recycling of eIF2:GDP / methionyl-initiator methionine tRNA binding / PERK regulates gene expression / eukaryotic translation initiation factor 2 complex / cytoplasmic translational initiation / translation factor activity, RNA binding / formation of translation preinitiation complex ...eukaryotic translation initiation factor 2 complex assembly / Cellular response to mitochondrial stress / Response of EIF2AK1 (HRI) to heme deficiency / Recycling of eIF2:GDP / methionyl-initiator methionine tRNA binding / PERK regulates gene expression / eukaryotic translation initiation factor 2 complex / cytoplasmic translational initiation / translation factor activity, RNA binding / formation of translation preinitiation complex / protein-synthesizing GTPase / Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition / Translation initiation complex formation / Response of EIF2AK4 (GCN2) to amino acid deficiency / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / translation initiation factor activity / protein folding chaperone / translational initiation / PKR-mediated signaling / ABC-family proteins mediated transport / cadherin binding / GTPase activity / GTP binding / magnesium ion binding / extracellular exosome / ATP binding / cytoplasm / cytosol
Similarity search - Function
Cell division cycle protein 123 / D123 / Initiation factor eIF2 gamma, C-terminal / Initiation factor eIF2 gamma, domain 2 / Initiation factor eIF2 gamma, GTP-binding domain / Initiation factor eIF2 gamma, C terminal / : / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / Translation elongation factor EFTu-like, domain 2 / Elongation factor Tu domain 2 ...Cell division cycle protein 123 / D123 / Initiation factor eIF2 gamma, C-terminal / Initiation factor eIF2 gamma, domain 2 / Initiation factor eIF2 gamma, GTP-binding domain / Initiation factor eIF2 gamma, C terminal / : / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / Translation elongation factor EFTu-like, domain 2 / Elongation factor Tu domain 2 / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Translation protein, beta-barrel domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Translation initiation factor eIF2 assembly protein / Eukaryotic translation initiation factor 2 subunit 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.97 Å
AuthorsSchmitt, E. / Mechulam, Y. / Cardenal Peralta, C. / Fagart, J. / Seufert, W.
Funding support France, Germany, 3items
OrganizationGrant numberCountry
Centre National de la Recherche Scientifique (CNRS)UMR7654 France
Ecole polytechniqueUMR7654 France
German Research Foundation (DFG) Germany
Citation
#1: Journal: Acta Crystallogr D Biol Crystallogr / Year: 2012
Title: Towards automated crystallographic structure refinement with phenix.refine.
Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D.
History
DepositionJun 20, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 16, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2023Group: Author supporting evidence / Structure summary / Category: pdbx_audit_support / struct / Item: _struct.title
Revision 1.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.3Oct 23, 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: Cell division cycle protein 123 homolog
B: Eukaryotic translation initiation factor 2 subunit 3
C: Cell division cycle protein 123 homolog
D: Eukaryotic translation initiation factor 2 subunit 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,8806
Polymers107,8664
Non-polymers1,0142
Water3,513195
1
A: Cell division cycle protein 123 homolog
B: Eukaryotic translation initiation factor 2 subunit 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,4403
Polymers53,9332
Non-polymers5071
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5150 Å2
ΔGint-20 kcal/mol
Surface area20060 Å2
MethodPISA
2
C: Cell division cycle protein 123 homolog
D: Eukaryotic translation initiation factor 2 subunit 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,4403
Polymers53,9332
Non-polymers5071
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5300 Å2
ΔGint-22 kcal/mol
Surface area20410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.259, 125.340, 74.081
Angle α, β, γ (deg.)90.000, 90.060, 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 Cell division cycle protein 123 homolog / Protein D123 / HT-1080 / PZ32


Mass: 41489.711 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDC123, C10orf7, D123 / Production host: Escherichia coli (E. coli) / References: UniProt: O75794
#2: Protein Eukaryotic translation initiation factor 2 subunit 3 / Eukaryotic translation initiation factor 2 subunit gamma X / eIF-2-gamma X / eIF-2gX


Mass: 12443.290 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EIF2S3, EIF2G / Production host: Escherichia coli (E. coli) / References: UniProt: P41091, protein-synthesizing GTPase
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 195 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.59 Å3/Da / Density % sol: 52.58 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 20% PEG3350, 8% tacsimate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.978 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 10, 2017
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.97→60.26 Å / Num. obs: 58305 / % possible obs: 94.1 % / Redundancy: 7 % / CC1/2: 0.997 / Rrim(I) all: 0.078 / Net I/σ(I): 13.7
Reflection shellResolution: 1.974→2.156 Å / Redundancy: 6.9 % / Num. unique obs: 2915 / CC1/2: 0.65 / Rrim(I) all: 1.098 / % possible all: 63.7

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MAD / Resolution: 1.97→60.26 Å / Cross valid method: FREE R-VALUE / σ(F): 38.23 / Phase error: 25.702
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2216 2999 5.14 %
Rwork0.1862 55306 -
obs0.1892 58305 75.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.5 Å2
Refinement stepCycle: LAST / Resolution: 1.97→60.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6550 0 62 195 6807
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00526777
X-RAY DIFFRACTIONf_angle_d0.73559164
X-RAY DIFFRACTIONf_chiral_restr0.0481995
X-RAY DIFFRACTIONf_plane_restr0.00571153
X-RAY DIFFRACTIONf_dihedral_angle_d19.09842495
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.97-2.010.479910.423559X-RAY DIFFRACTION1.54
2.01-2.040.5877170.4279270X-RAY DIFFRACTION7.04
2.04-2.080.435300.3661579X-RAY DIFFRACTION14.96
2.08-2.130.3473390.3193964X-RAY DIFFRACTION24.99
2.13-2.170.3245890.31981448X-RAY DIFFRACTION37.41
2.17-2.220.2717980.28811971X-RAY DIFFRACTION51.46
2.22-2.280.32231470.26542638X-RAY DIFFRACTION68.64
2.28-2.340.32531710.27253435X-RAY DIFFRACTION89.76
2.34-2.410.29591750.2613686X-RAY DIFFRACTION95.44
2.41-2.490.29971990.24633620X-RAY DIFFRACTION94.79
2.49-2.580.27762100.23683653X-RAY DIFFRACTION94.54
2.58-2.680.2821690.23553682X-RAY DIFFRACTION95.61
2.68-2.80.29841880.22783645X-RAY DIFFRACTION95.1
2.8-2.950.28622030.21313665X-RAY DIFFRACTION94.75
2.95-3.130.26231870.2123652X-RAY DIFFRACTION95.08
3.13-3.370.25191950.1983686X-RAY DIFFRACTION94.98
3.37-3.710.20411760.17523688X-RAY DIFFRACTION95.42
3.71-4.250.17281960.13913672X-RAY DIFFRACTION94.91
4.25-5.360.1631790.12893704X-RAY DIFFRACTION95.34
5.36-60.260.18021930.1773726X-RAY DIFFRACTION94.79
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)
14.594292221761.47299752809-1.006251451091.83293830402-1.191643257742.05586162163-0.0718500912111-0.0179157530472-0.205849857277-0.0273374293790.00411838687006-0.2031640024480.1742226377940.2406025816930.09975383819020.2008589300020.0494835214376-0.01280709195890.1994148076290.0428449346140.18009503632719.38302750798.896028449743.0200349062
23.443036549350.4286140992940.2746220887552.20387813339-0.1950386079291.98919495116-0.0361954556344-0.2635937559010.3248307402710.245142334050.1449145425130.344241827151-0.167169996218-0.3833323360280.02133328062040.1561569594580.02861862280740.02600095933420.1784723978020.0390407865260.1479728967825.8704550049614.8420530348.9147536961
33.209713200940.919661111375-0.7289047787581.34298687766-0.5553916086083.64770848511-0.2466639716840.311409358135-0.190210688307-0.1238455540880.009812201475320.03779042033520.451268450762-0.02009123802970.1737855671550.264245955050.0004369926825460.02306912155720.2641720457060.02279904448330.20698464010117.56139937759.7012687783135.4961259523
42.31215307645-0.5241521799080.3733591383664.15926274593-0.7271158084124.03157323715-0.1264929059150.6349742666990.33306980035-0.4749296952340.04944229684040.0434338177877-0.1601538803090.1040908142020.09962243496820.230036052255-0.0519591898964-0.03174350883350.3752479906520.1507809409550.2399249375523.172474556521.566188550125.3037976743
50.3408655555041.17198913168-1.405622522415.58256821851-6.495728746917.58900840503-0.0832290133009-0.1371719763120.0200343846816-1.166518070850.198871914136-0.02115373790581.000357782120.00886081773086-0.02984931192270.69771321322-0.0310671696578-0.08271477826450.539541527639-0.01253170515630.31680981907623.916115878417.38210406079.62787184748
66.02679793932.2240599773-2.408184400633.83874033547-2.599299906144.29373645310.1838054393750.2589600814920.173624798107-0.177073950493-0.1187138684910.0952832745061-0.451213604125-0.0969936222382-0.152869316660.5217457857840.0652899422953-0.1214040772480.4873650595130.03620542412240.2175162553139.1327223212916.943951631322.1226576669
77.18287171325-5.07323528351.349432833336.66483280191-0.2511258925693.878149340840.3658822764560.856019810257-0.373745185556-0.857069415695-0.1781906069491.172679837980.539649669501-1.03138352263-0.212929973610.4285212693830.0627575986101-0.09475670705210.651349720723-0.06588306778550.444430595845-18.55087689390.18005351700531.2333417807
84.10220726937-1.04316946830.1878566858494.89112257185-0.3384566215242.62029091447-0.162913744931-0.07695276077210.673921584819-0.15410540560.3708440841841.20772841282-0.251894318262-0.386661428011-0.1867213452740.2785360916230.0387899152136-0.09553318506170.4125464640410.07186804687220.446609476209-17.574423918717.016023406342.8190933324
92.81192795728-0.5723938872511.103370463871.474587197862.844444590027.369003122410.0202588063250.04505150865-1.50300781910.09504737737490.08245345085810.1214670110571.02037638019-0.402577202578-0.07487180107850.449549731382-0.0679965979484-0.1058367948120.344502641942-0.01615361140250.843578451948-11.682490203-6.1421283393338.3830157654
107.5131002232-0.0220502526854-0.2108726483777.36318062801-1.293646138086.35745961057-0.0623890333124-0.348369884819-0.1265960321450.1161412319190.01006784084610.153440840885-0.0256875445284-0.07957428049060.002472320556510.182008913720.0326048772146-0.03792912184710.2719556933280.07061074557210.255644508182-11.489120748610.026467233945.7597460894
116.274123635063.13765059722-0.1821997980073.669405330811.511672565961.24107848180.1585241775811.160579033540.95895986442-0.4948561239210.08002997668480.502292836154-0.1820505823980.02895436530210.05998776564670.2890579653660.0134484464441-0.1229072899560.3126993212020.09817047768360.4520564561-13.455666911920.874276579639.1659651615
123.06383535039-4.420535796641.001259877457.42221485970.06183505037035.403013096540.3951214819130.504191886318-0.375321765034-0.302494102063-0.2565177352540.2276740889690.4214694384450.0469423799118-0.1456630749670.210726018254-0.0257969661141-0.02891611165790.2182201004860.06260837613450.25325869245-8.687512896425.2368867189338.854684738
136.019965236543.513164929281.583058755083.742362163531.527357310416.1540796018-0.227628155111-0.159787486311.64305063653-0.4498603393120.5021894952791.0851585327-0.803864614426-0.490023266488-0.1216326616040.6207907397020.171745783508-0.03084274385020.318316659280.05221428019740.691021836034-19.027374068321.645252195246.7575472418
142.80803350367-0.7272116739060.6154642434891.6525250498-0.6620632397641.569735161230.06546068178110.2251147388510.170220434622-0.0968662850604-0.01859735296630.0463588155738-0.07397319685140.02603203890480.3313963999610.1865474560470.001770561917780.006925547176740.1812952597680.08712642117950.17782717430625.6926083797-12.3605630716-9.46734884152
152.51426328195-1.58452474061.399216245661.51476494799-0.7157288199835.02523882899-0.203800765222-0.103244437270.3243835387170.192181526450.0519750668227-0.0332661398426-0.670808272662-0.0768431952390.09495964910420.238562974061-0.000847780908358-0.0243909306010.2642403328590.05028586983060.29641095262733.0039657809-10.42323829251.57316891787
164.346889476960.592632020585-0.3320857196634.49529476091-0.3796713323235.14520434082-0.0305549871538-0.216976483924-0.05540777939190.320133450153-0.03422736439970.07767201821580.05825959768510.02439688244450.04902049526750.2448340203820.0269010166951-0.01600004560860.2559369225720.09644794746330.21358483572338.5243832722-22.428708096811.6448071008
173.40054520392-2.676813286112.548734438573.159238715590.03994620203865.7297309421-0.548429290794-0.07055944485530.1352929776081.436451632310.434935521432-0.457431641103-1.373877554510.2639380922440.110421491580.725797237526-0.0192566478766-0.07044698556440.390406789062-0.06201841518710.35956588076439.2772939409-18.652046008227.6463806933
186.36152815914-4.438943025944.12105158953.94725689189-3.063173503454.58511428884-0.132978254406-0.110064508822-0.3913402213640.2110627436760.137502297160.3131446352250.0646442374626-0.311061392199-0.2160486447110.504046415826-0.04772432261910.08576862462910.5210688732550.07344331357790.28420443965925.2835917195-18.376166577615.5209116112
194.610710932053.815852201760.1796866418266.39317596546-1.254730240283.489607876990.248231863405-1.20228960950.4850626736761.386561590450.3638045221571.63004161653-0.921758126477-1.12039734314-0.5268863195980.597592039052-0.002882420076820.2165081304760.790713699121-0.05190674365160.66645266612-2.86952879358-2.136362278216.4173448063
203.901189936571.72732710169-0.7633479936736.854799464161.129418215185.13625765733-0.06063669280940.0329251404457-0.5575876960240.06660876146390.1697403723931.079400139340.441971874696-0.760744632079-0.176992582080.260917665993-0.06371713812380.02061533124180.4099807053040.1367552702820.451838701345-1.86548367198-17.603912938-6.04626166785
216.072063516853.979573188210.01567318366433.118650069771.708484131855.6569002444-0.0981065987983-0.5204143388551.983969179830.2807991386370.4415410856490.675002900421-1.98463526611-0.846082795023-0.2938385997230.6916983842810.1802885140850.1441165746770.426611762389-0.107388835350.8938940388882.541050331764.65478802072-0.157729315038
225.25313024945-1.33881930486-0.9557636967816.670598558464.679376598997.508049703340.150083571545-0.04093028344060.96914808307-0.6049405768390.3089693609290.489269332239-1.07602042981-0.249348662401-0.4167403758370.351332785334-0.006266829225760.1098787066020.2933395845280.1611077282240.5231517865995.59314985768-0.59257067468-8.70109640929
237.954311384610.2173097217460.008007818619338.45172559164-1.767234323674.83837711919-0.0819269545235-0.507279617863-0.3714256143220.4076877885520.05954543251590.0255362703795-0.203284314314-0.0165022851381-0.05764119542960.1983995017620.00265993076990.04976920567870.2894870287140.1269971877580.2878771548575.98051367829-13.9164785548-4.62507353553
245.4928081193-5.374754892431.449145473795.32408982864-1.10876491913.662622052570.4273812228860.4949679229370.575720183053-0.6112089577740.1503282110840.5229292500340.044370647881-0.703163434289-0.2824886355820.1911772490290.00279917187977-0.06141804115280.3099655018820.2023995229520.522478738411-1.99411652709-11.7072801771-11.5152604526
255.018875339220.187624683459-0.5126145781511.936992432840.3596809154113.72614370684-0.136267424566-0.358939073837-0.2041766529060.2909852377070.1366519927820.2818798425160.0637003523904-0.144598542177-0.002242965242240.2714680154420.04792274771450.02050790097390.3634704469410.1382764977090.3114887920115.5703932707-13.0185619771-2.48731553716
266.174730967491.5214426955-0.4798740021354.514147837420.3878832719324.37601728684-0.00829420954076-0.7398006062150.569898103180.3068977361320.2447107990090.277186346316-0.156710750919-0.250842098341-0.08128770788460.2598954846710.0634329970178-0.001157289503790.2526697316820.0588608042190.2542524161894.47793290092-6.59447726764-0.803863560725
279.14109636339-7.34025230093-2.868584970726.124536774863.427000055977.19777306822-0.4881869030910.122072636912-1.672938359790.1118660482370.8835368386691.980962003930.900910492867-0.400644242495-0.1662237460310.442479118637-0.1236117341540.006356164145190.4128958004820.1385616723450.715029897445-2.4502708578-24.3551066878-9.4454199938
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 48 )AA1 - 481 - 48
22chain 'A' and (resid 49 through 136 )AA49 - 13649 - 115
33chain 'A' and (resid 137 through 183 )AA137 - 183116 - 162
44chain 'A' and (resid 184 through 260 )AA184 - 260163 - 239
55chain 'A' and (resid 261 through 280 )AA261 - 280240 - 259
66chain 'A' and (resid 281 through 318 )AA281 - 318260 - 284
77chain 'A' and (resid 319 through 336 )AA319 - 336285 - 302
88chain 'B' and (resid 362 through 376 )BC362 - 3761 - 15
99chain 'B' and (resid 377 through 395 )BC377 - 39516 - 25
1010chain 'B' and (resid 396 through 429 )BC396 - 42926 - 59
1111chain 'B' and (resid 430 through 439 )BC430 - 43960 - 69
1212chain 'B' and (resid 440 through 459 )BC440 - 45970 - 89
1313chain 'B' and (resid 460 through 465 )BC460 - 46590 - 95
1414chain 'C' and (resid -2 through 136 )CD-2 - 1361 - 123
1515chain 'C' and (resid 137 through 183 )CD137 - 183124 - 170
1616chain 'C' and (resid 184 through 260 )CD184 - 260171 - 247
1717chain 'C' and (resid 261 through 280 )CD261 - 280248 - 267
1818chain 'C' and (resid 281 through 318 )CD281 - 318268 - 291
1919chain 'C' and (resid 319 through 335 )CD319 - 335292 - 308
2020chain 'D' and (resid 363 through 376 )DF363 - 3761 - 14
2121chain 'D' and (resid 377 through 381 )DF377 - 38115 - 19
2222chain 'D' and (resid 382 through 404 )DF382 - 40420 - 34
2323chain 'D' and (resid 405 through 420 )DF405 - 42035 - 50
2424chain 'D' and (resid 421 through 429 )DF421 - 42951 - 59
2525chain 'D' and (resid 430 through 449 )DF430 - 44960 - 79
2626chain 'D' and (resid 450 through 459 )DF450 - 45980 - 89
2727chain 'D' and (resid 460 through 466 )DF460 - 46690 - 96

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