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- PDB-8vza: Crystal Structure of 2-Hydroxacyl-CoA Lyase/Synthase ApbHACS from... -

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Basic information

Entry
Database: PDB / ID: 8vza
TitleCrystal Structure of 2-Hydroxacyl-CoA Lyase/Synthase ApbHACS from Alphaproteobacteria bacterium in the Complex with THDP, L-Lactyl-CoA, and ADP
Components2-Hydroxyacyl-CoA lyase/Synthase
KeywordsLYASE / 2-hydroxyacyl-CoA lyase/synthase / acyloin condensation / oxalyl-CoA decarboxylase / SBC / eBERlight
Function / homology
Function and homology information


oxalyl-CoA decarboxylase / oxalyl-CoA decarboxylase activity / fatty acid alpha-oxidation / thiamine pyrophosphate binding / nucleotide binding / magnesium ion binding
Similarity search - Function
TPP-binding domain containing protein HACL1-like / TPP-binding enzyme, conserved site / Thiamine pyrophosphate enzymes signature. / Thiamine pyrophosphate enzyme, central domain / Thiamine pyrophosphate enzyme, central domain / Thiamine pyrophosphate enzyme, N-terminal TPP-binding domain / Thiamine pyrophosphate enzyme, N-terminal TPP binding domain / Thiamine pyrophosphate enzyme, C-terminal TPP-binding / Thiamine pyrophosphate enzyme, C-terminal TPP binding domain / Thiamin diphosphate-binding fold / DHS-like NAD/FAD-binding domain superfamily
Similarity search - Domain/homology
Chem-8FL / ACETYL GROUP / ADENOSINE-5'-DIPHOSPHATE / : / Oxalyl-CoA decarboxylase
Similarity search - Component
Biological speciesAlphaproteobacteria bacterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsGade, P. / Kim, Y. / Endres, M. / Lee, S. / Yoshikuni, Y. / Gonzalez, R. / Michalska, K. / Joachimiak, A.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States) United States
CitationJournal: Commun Chem / Year: 2024
Title: Revealing reaction intermediates in one-carbon elongation by thiamine diphosphate/CoA-dependent enzyme family.
Authors: Kim, Y. / Lee, S.H. / Gade, P. / Nattermann, M. / Maltseva, N. / Endres, M. / Chen, J. / Wichmann, P. / Hu, Y. / Marchal, D.G. / Yoshikuni, Y. / Erb, T.J. / Gonzalez, R. / Michalska, K. / Joachimiak, A.
History
DepositionFeb 11, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 2-Hydroxyacyl-CoA lyase/Synthase
B: 2-Hydroxyacyl-CoA lyase/Synthase
C: 2-Hydroxyacyl-CoA lyase/Synthase
D: 2-Hydroxyacyl-CoA lyase/Synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)247,00725
Polymers239,8054
Non-polymers7,20221
Water14,232790
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23390 Å2
ΔGint-134 kcal/mol
Surface area67270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.409, 102.679, 104.344
Angle α, β, γ (deg.)114.100, 96.740, 105.230
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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Protein , 1 types, 4 molecules ABCD

#1: Protein
2-Hydroxyacyl-CoA lyase/Synthase


Mass: 59951.207 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Alphaproteobacteria bacterium (bacteria)
Gene: DCO82_10540 / Plasmid: p53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold / References: UniProt: A0A3C0TX30, oxalyl-CoA decarboxylase

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Non-polymers , 7 types, 811 molecules

#2: Chemical
ChemComp-8FL / 2-[(2R)-3-[(4-azanyl-2-methyl-pyrimidin-5-yl)methyl]-4-methyl-2-oxidanyl-2H-1,3-thiazol-5-yl]ethyl phosphono hydrogen phosphate


Mass: 442.322 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H20N4O8P2S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-UQ3 / S-{(3S,5R,9R)-1-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)oxolan-2-yl]-3,5,9-trihydroxy-8,8-dimethyl-3,5,10,14-tetraoxo-2,4,6-trioxa-11,15-diaza-3lambda~5~,5lambda~5~-diphosphaheptadecan-17-yl} (2R)-2-hydroxypropanethioate / Lactyl-CoA


Mass: 839.597 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C24H40N7O18P3S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#5: Chemical
ChemComp-ACE / ACETYL GROUP


Mass: 44.053 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H4O
#6: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#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
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 790 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Nonpolymer detailsThe authors state that the 2-[(2R)-3-[(4-azanyl-2-methyl-pyrimidin-5-yl)methyl]-4-methyl-2-oxidanyl- ...The authors state that the 2-[(2R)-3-[(4-azanyl-2-methyl-pyrimidin-5-yl)methyl]-4-methyl-2-oxidanyl-2H-1,3-thiazol-5-yl]ethyl phosphono hydrogen phosphate ligand is in an intermediate or transition state.

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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: 2.64 Å3/Da / Density % sol: 53.43 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1 M TrisHCl pH 7.0, 20 % (w/v) PEG2000MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Mar 24, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 144733 / % possible obs: 94.9 % / Redundancy: 3.5 % / Biso Wilson estimate: 25.36 Å2 / CC1/2: 0.928 / Rmerge(I) obs: 0.189 / Rpim(I) all: 0.116 / Rrim(I) all: 0.223 / Net I/σ(I): 7.92
Reflection shellResolution: 2.05→2.09 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.671 / Mean I/σ(I) obs: 1.44 / Num. unique obs: 5583 / CC1/2: 0.49 / Rpim(I) all: 0.471 / Rrim(I) all: 0.823 / % possible all: 73.2

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→49.52 Å / SU ML: 0.2797 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 25.1724
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2427 7055 4.88 %
Rwork0.2067 137397 -
obs0.2085 144452 94.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.56 Å2
Refinement stepCycle: LAST / Resolution: 2.05→49.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16633 0 438 790 17861
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003617513
X-RAY DIFFRACTIONf_angle_d0.772823845
X-RAY DIFFRACTIONf_chiral_restr0.04652547
X-RAY DIFFRACTIONf_plane_restr0.00643159
X-RAY DIFFRACTIONf_dihedral_angle_d13.8026455
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.080.32651550.25852960X-RAY DIFFRACTION61.25
2.08-2.10.31282020.25793883X-RAY DIFFRACTION79.18
2.1-2.130.29092430.24644460X-RAY DIFFRACTION92.82
2.13-2.150.3042320.24374567X-RAY DIFFRACTION93.77
2.15-2.180.30212440.24744555X-RAY DIFFRACTION94.79
2.18-2.210.31572330.23814612X-RAY DIFFRACTION95.02
2.21-2.240.2912590.22984672X-RAY DIFFRACTION95.45
2.24-2.280.27632440.23444606X-RAY DIFFRACTION95.55
2.28-2.310.27222240.22544679X-RAY DIFFRACTION95.82
2.31-2.350.27082330.22144567X-RAY DIFFRACTION94.96
2.35-2.390.25932380.21284676X-RAY DIFFRACTION94.72
2.39-2.430.24242270.20814537X-RAY DIFFRACTION94.09
2.43-2.480.27272430.20954610X-RAY DIFFRACTION94.2
2.48-2.530.26162430.20294592X-RAY DIFFRACTION96.6
2.53-2.590.27542220.21154783X-RAY DIFFRACTION96.86
2.59-2.650.29892330.21244686X-RAY DIFFRACTION96.74
2.65-2.710.2572500.20264661X-RAY DIFFRACTION96.33
2.71-2.790.24481880.20854743X-RAY DIFFRACTION96.59
2.79-2.870.2542380.21734693X-RAY DIFFRACTION96.42
2.87-2.960.26662670.22224644X-RAY DIFFRACTION96.16
2.96-3.070.29212550.21744649X-RAY DIFFRACTION95.78
3.07-3.190.25352200.21254757X-RAY DIFFRACTION97.66
3.19-3.340.24972440.20974737X-RAY DIFFRACTION97.61
3.34-3.510.24062350.20844724X-RAY DIFFRACTION97.6
3.51-3.730.22822270.194765X-RAY DIFFRACTION97.5
3.73-4.020.20082460.18334676X-RAY DIFFRACTION96.19
4.02-4.420.19472330.17684787X-RAY DIFFRACTION98.35
4.42-5.060.20292740.17294716X-RAY DIFFRACTION97.88
5.06-6.380.19072550.20234676X-RAY DIFFRACTION96.46
6.38-49.520.21082480.20994724X-RAY DIFFRACTION97.26
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)
10.7158471402380.4575248542150.185433673270.8323684739130.1429042336520.8958987933880.0885270289966-0.04219522924610.0713632389402-0.0475371798608-0.0821701596070.072367525006-0.0656712700678-0.197754711413-0.0142932493740.1387748694080.006267250197960.001865650237140.200163961131-0.0106333629380.142048645146-14.689545646318.3429596938-3.05673832808
21.85051570784-0.767382695930.1060229427072.136876361680.8096238131683.62305269466-0.114850536895-0.149048690682-0.1116583391310.2205449363480.02893265140720.2358599448490.222433574911-0.1300755208040.0646908163330.1535678650770.004994570317940.02361271811090.1577445803730.0166659392030.156314888288-12.994206374810.31344944464.71010902938
31.98130941490.9067521981161.839628462790.7503924547810.8097933848721.91768283072-0.00383373448751-0.2147488701010.2040232437210.154323429309-0.09808690056040.182112506790.0430477056728-0.1802422674130.0894623483670.2204323030150.01461900025860.02555763835480.187524091068-0.02888533272620.196390843835-1.3058696565322.714700507619.8755766541
41.24213627095-1.49368383779-1.939588740152.597214420092.109837761378.433870130720.1904864867370.1393898163540.130134945585-0.357357803871-0.0656230631962-0.0532874254125-0.583021106043-0.13171491198-0.08755002529070.169580556767-0.02744936594030.01377515159320.1740948724470.02200524444040.2165976721229.9692147776235.837720932918.7343976215
50.496196626015-0.195449369032-0.8077856814272.987709463290.3773886026162.88903946478-0.110702780405-0.05856730164170.002475698658540.1120369704370.107910127926-0.07805680217870.03884086207910.106800242640.01218736151060.128669145288-0.00553223016253-0.03430692241030.227809788312-0.02484036932060.12804343739317.791673381423.17476740416.9034131824
60.9888006758860.455105715184-0.3731241199660.786149627624-0.08735431577252.32670202020.111998348398-0.1999742322460.184941023920.0939189121223-0.07967858885190.00770876087495-0.3221791239660.317273706919-0.04159506565760.197716009617-0.0144472336946-0.008291811387820.158730913732-0.03456769362530.16482927588418.969976780137.223059040420.7986089083
71.409727226730.66325922682-0.01849876583381.04380926882-0.1141185018121.1048865725-0.05033305963540.05723652405870.221728423164-0.04046789190770.02677223214540.0199723584787-0.387185714887-0.01783190076070.003319115205390.277867283397-0.00750956786963-0.03608063073950.1510090564710.02355740266660.2054378097648.4639833291736.9345606388-1.82872546897
85.83272277871-0.7700879001270.6837144505533.13323665969-0.3121671466470.722755467407-0.1776462691030.2035370751180.147623710542-0.2312266407470.143764577744-0.0516764576706-0.1691917301730.04234645226250.02660346149670.265955963722-0.0278744022959-0.009870443924220.206160770618-0.007602021917770.1054023902294.8604698204432.7870085354-12.5232573942
91.09620148454-0.6257337327070.913423388055.38673963782-1.063128953981.145937469380.2270206332850.446167208760.398936998939-0.649458333923-0.259341777692-0.45012501016-0.2046694396530.152642512147-0.004029053952230.308710369318-0.0632154369426-0.01223699718150.2837015673890.05302943951580.1595942770439.7533047054834.9463192907-21.206444358
101.59071966034-0.05561878892840.6973964441190.340912009227-0.5122569705680.821561059351-0.3400897002490.1430177231220.3971069630590.05724422133740.0290162188138-0.309165161178-0.3112238802690.1405333877350.2841166779360.348173294893-0.081233716360.011556572440.1816197396440.00491981914940.27804504819913.896741462138.7427646939-8.47670503812
110.679253010468-0.175896525653-0.6279916261820.329792992804-0.008890719265251.02501697353-0.017081284944-0.0150469171032-0.04468926525680.0318049954865-0.0101816018592-0.02744877471490.007563509385890.1113236194940.0351150590190.129945805845-0.0162827409852-0.001330108635520.1745863982020.00501779489240.17784116181714.28114902096.7623079121-14.4432106869
120.2008595466570.2039371299570.388089585220.7092668568710.01681941764880.7695430164480.0154944589340.0624799324524-0.042822543591-0.0296505977810.01506004778240.02867245559310.077451832752-0.00720988501024-0.03287150218910.181826435076-0.0109577229080.02742508858070.247411859506-0.01872215000210.159811445194-11.8914055746-6.47785218108-33.2317575952
131.53713919176-0.1199029554520.3545400317340.775258987224-0.08169599061360.597528954888-0.03389019813520.1108422882480.141741837692-0.07858638175420.01296593697990.0417429091077-0.1056301262190.01693829322380.03410684871340.231642952237-0.01120345940210.01392689105010.2061180024150.01267215083740.151819936885-8.6857681747921.9552632936-30.076533486
141.057885290030.0391291290586-0.1000600175990.9188215740240.1486792586060.7825178080850.03699319093050.007207874898480.0475056060040.0142301344938-0.003740560151590.00165071152423-0.0429302879098-0.0828109200176-0.03645787965930.152103250031-0.009712619570660.005560369057550.1639480099610.01105086555070.132552987411-14.5623230162-16.20587451210.887424382817
153.28352440111-1.28294764326-2.51700184330.9044580076480.9077980631072.065136193760.1720729855270.433955832913-0.142666114649-0.231142183123-0.1835053684890.11848760791-0.0909585095172-0.3047047383520.00833002771370.2821016382150.0034696182685-0.04086426194420.189185246543-0.0222600435560.217574649658-0.694066648519-23.1255804003-20.4565007581
162.632745955520.6515182714370.5893353830121.578807602960.03016624491962.613124972720.01096238246010.05884369875480.0890542449351-0.163823097838-0.0387772879824-0.0479384808727-0.1074551541440.00180931439670.02704291036640.1941389448210.03846494185940.002919864575510.142992080958-0.01671255782410.16171472001115.2789496323-27.3018769501-17.4965263789
170.57073039183-0.521996345525-0.1524704067450.667664920102-0.2454197454250.623726402107-0.0298955417353-0.0256833290788-0.02556700545980.06890416580370.0227879872212-0.09789269463540.2017741829040.04851922276130.003502811039020.251808422943-0.00269608378185-0.03193810130070.166243439985-0.008721783606530.23018997269912.3096951953-37.2867426294-6.56467224817
182.135375533770.672775721098-0.7347229681751.17178868323-0.4181920198211.24353956180.0212079912807-0.20497054712-0.07595275068620.156681380174-0.000305018578719-0.02853937399880.1617851557970.119090526175-0.01224453185030.2582514174830.0323777011452-0.0173920164380.1809395044950.01239833614940.1888786230649.28862983674-35.754679858213.5797784154
191.00324803216-0.2403446912290.2870797915150.6131246053950.3132680142471.17339146519-0.0006752970235060.00438278345583-0.05442699536370.01814622774320.0223453307282-0.09196541012430.007222710602850.159127336859-0.01051235692510.133060397499-0.01575724819590.001327602519910.1742140034760.01189012173610.13999229863814.84303613-10.117606764415.8030157431
202.10713942789-0.6656744361620.1894725954661.851365461671.330875468762.705218846360.04930509034210.2524070320460.208255046744-0.2117562496430.0167180756686-0.168934760704-0.2244925113750.222284707732-0.05699623489460.188703557821-0.01535298755230.01142105678720.1941637428710.04363072034720.18421517499913.19587674610.18880226892111.4321543102
212.45362548224-1.00028601429-1.94741235850.7139988289520.9651047729771.467810006540.086067295662-0.2828657598770.232813473287-0.06235088234560.0707057120554-0.0885832159321-0.1213613530730.25109958025-0.1493951387760.221015796777-0.0140306874226-0.03071715472560.311581907032-0.01101467979840.1624062600671.340067132249.3621940198228.7413210653
222.297053483080.202023306693-0.4917297824122.610550413890.8354993113582.24387703334-0.0404648302024-0.05605340393980.00576852283840.110612036781-0.01889674827440.05398125418520.0344466815494-0.1559131893070.07250367486460.165775793807-0.008091805437090.00786523539170.19083000261-0.00482898783630.113650873314-15.17570573615.4815225227631.7703973968
230.4028912594990.0125370027236-0.3820523080880.382835701458-0.05860939647140.443348188838-0.0174103551419-0.0966295043492-0.01898010383640.1042147095040.0240207685278-0.002500335417340.08951830380220.0006578592082710.003176893046440.251096790746-0.002396568018830.002084698308620.248002207870.01821208807010.150729049456-12.1739551206-8.4528173903436.7839527325
242.00519372449-0.9920928723740.08807168534991.6052565178-0.3405836038631.63463625794-0.05250762540860.129813076496-0.20068851476-0.1262061263690.03209501070680.0619146173380.240826714795-0.06811256315950.02827971405810.264395333639-0.0404456869726-0.0006436304939910.1638204975250.02930606491250.151611571705-8.87096346796-26.326532315527.7522396767
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid -2 through 120 )AA-2 - 1201 - 123
22chain 'A' and (resid 121 through 169 )AA121 - 169124 - 172
33chain 'A' and (resid 170 through 223 )AA170 - 223173 - 226
44chain 'A' and (resid 224 through 250 )AA224 - 250227 - 253
55chain 'A' and (resid 251 through 318 )AA251 - 318254 - 321
66chain 'A' and (resid 319 through 363 )AA319 - 363322 - 366
77chain 'A' and (resid 364 through 438 )AA364 - 438367 - 441
88chain 'A' and (resid 439 through 481 )AA439 - 481442 - 484
99chain 'A' and (resid 482 through 515 )AA482 - 515485 - 515
1010chain 'A' and (resid 516 through 554 )AA516 - 554516 - 554
1111chain 'B' and (resid -2 through 169 )BF-2 - 1691 - 172
1212chain 'B' and (resid 170 through 363 )BF170 - 363173 - 366
1313chain 'B' and (resid 364 through 554 )BF364 - 554367 - 553
1414chain 'C' and (resid -5 through 170 )CL-5 - 1701 - 176
1515chain 'C' and (resid 171 through 223 )CL171 - 223177 - 229
1616chain 'C' and (resid 224 through 318 )CL224 - 318230 - 324
1717chain 'C' and (resid 319 through 438 )CL319 - 438325 - 444
1818chain 'C' and (resid 439 through 554 )CL439 - 554445 - 557
1919chain 'D' and (resid -2 through 120 )DQ-2 - 1201 - 123
2020chain 'D' and (resid 121 through 169 )DQ121 - 169124 - 172
2121chain 'D' and (resid 170 through 223 )DQ170 - 223173 - 226
2222chain 'D' and (resid 224 through 318 )DQ224 - 318227 - 321
2323chain 'D' and (resid 319 through 438 )DQ319 - 438322 - 441
2424chain 'D' and (resid 439 through 554 )DQ439 - 554442 - 553

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