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- PDB-7z6z: Crystal structure of Angiotensin-1 converting enzyme N-domain in ... -

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Basic information

Entry
Database: PDB / ID: 7z6z
TitleCrystal structure of Angiotensin-1 converting enzyme N-domain in complex with fosinoprilat
ComponentsAngiotensin-converting enzyme, soluble form
KeywordsHYDROLASE / Angiotensin-1 converting enzyme / fosinoprilat / fosinopril / Metalloprotease
Function / homology
Function and homology information


mononuclear cell proliferation / cell proliferation in bone marrow / bradykinin receptor binding / exopeptidase activity / regulation of angiotensin metabolic process / substance P catabolic process / tripeptidyl-peptidase activity / peptidyl-dipeptidase A / regulation of renal output by angiotensin / negative regulation of gap junction assembly ...mononuclear cell proliferation / cell proliferation in bone marrow / bradykinin receptor binding / exopeptidase activity / regulation of angiotensin metabolic process / substance P catabolic process / tripeptidyl-peptidase activity / peptidyl-dipeptidase A / regulation of renal output by angiotensin / negative regulation of gap junction assembly / hormone catabolic process / bradykinin catabolic process / metallodipeptidase activity / regulation of smooth muscle cell migration / regulation of hematopoietic stem cell proliferation / neutrophil mediated immunity / hormone metabolic process / mitogen-activated protein kinase binding / mitogen-activated protein kinase kinase binding / chloride ion binding / arachidonate secretion / post-transcriptional regulation of gene expression / peptide catabolic process / heart contraction / positive regulation of systemic arterial blood pressure / regulation of heart rate by cardiac conduction / antigen processing and presentation of peptide antigen via MHC class I / regulation of systemic arterial blood pressure by renin-angiotensin / blood vessel remodeling / amyloid-beta metabolic process / hematopoietic stem cell differentiation / peptidyl-dipeptidase activity / regulation of vasoconstriction / Metabolism of Angiotensinogen to Angiotensins / angiotensin maturation / metallocarboxypeptidase activity / blood vessel diameter maintenance / angiotensin-activated signaling pathway / kidney development / regulation of synaptic plasticity / metalloendopeptidase activity / regulation of blood pressure / male gonad development / metallopeptidase activity / peptidase activity / actin binding / spermatogenesis / endopeptidase activity / calmodulin binding / lysosome / endosome / negative regulation of gene expression / external side of plasma membrane / proteolysis / extracellular space / extracellular exosome / extracellular region / zinc ion binding / plasma membrane
Similarity search - Function
Peptidase M2, peptidyl-dipeptidase A / Angiotensin-converting enzyme / Peptidase family M2 domain profile. / Neutral zinc metallopeptidases, zinc-binding region signature.
Similarity search - Domain/homology
ACETATE ION / fosinoprilat / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Angiotensin-converting enzyme
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsCozier, G.E. / Acharya, K.R.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/M026647/1 United Kingdom
CitationJournal: Febs J. / Year: 2022
Title: Structural basis for the inhibition of human angiotensin-1 converting enzyme by fosinoprilat.
Authors: Cozier, G.E. / Newby, E.C. / Schwager, S.L.U. / Isaac, R.E. / Sturrock, E.D. / Acharya, K.R.
History
DepositionMar 14, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 22, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 20, 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: Angiotensin-converting enzyme, soluble form
B: Angiotensin-converting enzyme, soluble form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,90953
Polymers144,9872
Non-polymers6,92351
Water12,845713
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A: Angiotensin-converting enzyme, soluble form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,47127
Polymers72,4931
Non-polymers3,97826
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Angiotensin-converting enzyme, soluble form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,43826
Polymers72,4931
Non-polymers2,94525
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.575, 77.800, 81.592
Angle α, β, γ (deg.)88.921, 64.616, 74.805
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, 2 molecules AB

#1: Protein Angiotensin-converting enzyme, soluble form


Mass: 72493.352 Da / Num. of mol.: 2
Mutation: N9Q, N25Q, N82Q, N117Q, N131Q, N289Q, Q545R, P576L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACE, DCP, DCP1 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P12821

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Sugars , 5 types, 6 molecules

#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 732.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1221m-1a_1-5]/1-1-2-3/a4-b1_a6-d1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#4: Polysaccharide alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-6DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#5: 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.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam 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
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#16: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 11 types, 758 molecules

#6: Chemical ChemComp-KS8 / fosinoprilat


Mass: 435.494 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H34NO5P / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C4H10O3
#8: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O4
#9: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#10: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H3O2
#11: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#12: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#13: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#14: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#15: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#17: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 713 / Source method: isolated from a natural source / Formula: H2O

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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: 2.75 Å3/Da / Density % sol: 55.34 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M Tris/Bicine pH 8.5, 0.06 M Divalent cations, 30% PEG550MME/PEG20000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Oct 21, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.75→73.29 Å / Num. obs: 152059 / % possible obs: 97.4 % / Redundancy: 7.1 % / Biso Wilson estimate: 25.24 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.135 / Rpim(I) all: 0.054 / Net I/σ(I): 8.2
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 6.5 % / Mean I/σ(I) obs: 0.8 / Num. unique obs: 7322 / CC1/2: 0.438 / % possible all: 94.2

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6F9V

6f9v


Resolution: 1.75→63.46 Å / SU ML: 0.2462 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 24.038
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1995 2101 1.38 %
Rwork0.1718 149830 -
obs0.1722 151931 97.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.97 Å2
Refinement stepCycle: LAST / Resolution: 1.75→63.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9878 0 445 713 11036
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007910769
X-RAY DIFFRACTIONf_angle_d0.864814615
X-RAY DIFFRACTIONf_chiral_restr0.04821526
X-RAY DIFFRACTIONf_plane_restr0.0081882
X-RAY DIFFRACTIONf_dihedral_angle_d15.03063960
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.790.3831520.34179676X-RAY DIFFRACTION94.33
1.79-1.840.29071400.30099917X-RAY DIFFRACTION96.03
1.84-1.890.31951400.26299764X-RAY DIFFRACTION95.92
1.89-1.940.26421280.241710003X-RAY DIFFRACTION96.66
1.94-20.25351370.23319876X-RAY DIFFRACTION96.74
2-2.070.24961390.21089996X-RAY DIFFRACTION96.92
2.07-2.160.26191120.19119933X-RAY DIFFRACTION96.87
2.16-2.260.23491330.17429980X-RAY DIFFRACTION97.42
2.26-2.380.17311380.167810002X-RAY DIFFRACTION97.53
2.38-2.520.20041460.165410088X-RAY DIFFRACTION97.92
2.52-2.720.19251500.16210065X-RAY DIFFRACTION98.16
2.72-2.990.19521550.15910057X-RAY DIFFRACTION98.29
2.99-3.430.19011360.157510128X-RAY DIFFRACTION98.72
3.43-4.320.14611340.133110182X-RAY DIFFRACTION99.06
4.32-63.460.18281610.159310163X-RAY DIFFRACTION99.31
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)
12.348023972481.61755938421-1.938743355732.14346237644-2.115865253633.418853334910.03196309007440.0373991820278-0.196676577632-0.1698260007480.03731956786410.2652482913290.173113853112-0.247796056229-0.1116165022420.2429038993430.0242312512862-0.04634301229920.290054605443-0.02418042334350.373706295433-24.738942078-25.0969097-23.1101630044
21.612065521110.0890234372195-1.050234578831.60842884159-0.2332734112570.764066648290.05660376683950.0373990042655-0.03450553811280.09152836562230.01822259564460.229360440252-0.0424855198659-0.209524956295-0.08760011074560.227665338084-0.0215420679846-0.06428654972570.275537933428-0.009280519828760.289542551086-23.3174579984-19.3176649251-17.3796387983
39.46544069481.23287567255-2.079016054941.15885741526-0.2718012209331.64827182153-0.03875449502060.4398247704350.106438392711-0.2698019469650.08227263861840.0124659127112-0.03103075644830.0781227770677-0.08432793962480.3245202409480.0180604572923-0.001198462626570.2550876739520.02381458200170.206587895609-3.59667479-1.46196798292-29.6759251712
43.047531114980.1559776547260.2276969559941.09275792025-0.1701148888020.7684191953850.0364858530398-0.1039506409490.0327008526426-0.005305211308570.00940469184007-0.00141398049963-0.0133992078175-0.00347817337712-0.04881421530160.218208758807-0.001963920709060.02017343509960.146089890167-0.06227460409080.1362759591581.29653890651-5.18931401046-12.718740123
52.72396165318-1.20709032693-0.6250164613741.65948640093-0.01226355073271.655042453720.1476514793720.07317767665370.0213160787172-0.141115886113-0.0998020606385-0.275343478751-0.09127367610270.183831909849-0.06114428144180.209730457348-0.02541365152480.04802530106430.2329852738280.01544373948010.28071325345620.3354612571-5.0904240927-20.297629707
62.10189424911-0.328635092991-0.7310368878911.96987767806-0.1369964569121.488262689990.07914467595620.276467032891-0.0519102293789-0.253171877554-0.0526746902392-0.0334323489567-0.0334949733386-0.064825755807-0.02360584001880.2375403252360.0256146281293-0.003472922954070.227514212456-0.03729529466820.1642808796632.00812488063-22.6304995245-32.4497946909
73.941211504150.607899043937-0.5026638477571.55828012652-0.1153128206991.26128477006-0.09638315048820.148551272429-0.279454014687-0.09632167385570.0363867330483-0.2664752821630.05442342365740.09351161452370.06052760946580.2096791947880.00975385936212-0.001206149982670.164601129433-0.01769816527690.1943662218977.86158066436-26.864532397-22.0297917208
81.80256920977-0.6466148760440.1192713029061.35607052218-0.07987624151510.4925451107710.0481408102385-0.006679484725220.0801374430726-0.00172997115746-0.00835093939118-0.0410938376929-0.071365625430.0138577163541-0.0383080300030.1969461286-0.02337410901970.01376084929820.1876470383560.001468998939990.1636228380324.31159390584-3.81555799472-13.8885821149
93.32186792906-1.176346775-0.9944974265713.082157972770.9617613238351.60676447555-0.0581551699892-0.135952218681-0.3577469129330.1851789966050.0703217267619-0.1423983737340.2236356484090.0836879575031-0.01159403602860.237517196130.00520613240771-0.04389140510380.2074771167860.02027710047150.2123241472525.86979243497-30.5242683435-13.4214003631
102.424799343990.8062684036480.3058855689193.331970896080.415525383850.2989393598950.01519717899880.07124157539940.0530032407094-0.01386946524410.0988368842431-0.415381493549-0.03306015933210.146082098067-0.09231334427990.191903410923-0.01309190121150.02627062054530.263686183299-0.03755272144530.13804932464818.6501674875-6.43238351051-9.89067661792
112.086911466681.68463545154-1.601102707893.65985316972-1.704003529681.19291992002-0.26312318833-0.144509907563-0.1285601976320.2737960189880.2257003965250.283734464940.207825722304-0.07709410902130.02531077289040.6313894763770.1319689178660.07929983159390.431393543440.04698410677410.3361100472230.386639844231-3.0535270662935.5693156894
120.893205844759-0.455120822621-0.06068847133311.84621200203-0.1559445878381.72184122766-0.0550109258478-0.0839551549111-0.04731099699830.1758596253380.043849587524-0.0234667881020.1181327341910.1031457777160.02186792979950.2176094221690.01247155482610.03453488754170.159623857453-0.04003972824860.1716898501735.2211563735812.853868601911.3727040267
130.834516204128-0.375681297629-0.3952643821941.461302810030.726294729821.36399743563-0.0380079519094-0.09915469284380.05107606747170.2326899408720.05646600655370.104340355634-0.0662784480623-0.0624350257105-0.02356415464350.2520287045510.007070373901410.04115377002820.1653190303530.002313226099460.202416581503-2.691313427922.228146405416.9372311504
141.32608368061-0.357142817855-1.016941039471.502286248190.2481612513032.86122691919-0.0608358129932-0.0139656585429-0.1528883451950.1910803818-0.1068087804350.424386652107-0.0218932374882-0.4213118760120.07898038846490.232231034737-0.02825962731240.0436027316120.221162770737-0.03695276541210.330158174302-14.336878297119.510799597711.3661287049
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 43 )AA1 - 431 - 43
22chain 'A' and (resid 44 through 104 )AA44 - 10444 - 104
33chain 'A' and (resid 105 through 152 )AA105 - 152105 - 147
44chain 'A' and (resid 153 through 237 )AA153 - 237148 - 232
55chain 'A' and (resid 238 through 279 )AA238 - 279233 - 274
66chain 'A' and (resid 280 through 371 )AA280 - 371275 - 366
77chain 'A' and (resid 372 through 417 )AA372 - 417367 - 412
88chain 'A' and (resid 418 through 498 )AA418 - 498413 - 493
99chain 'A' and (resid 499 through 560 )AA499 - 560494 - 555
1010chain 'A' and (resid 561 through 609 )AA561 - 609556 - 604
1111chain 'B' and (resid 1 through 104 )BAA1 - 1041 - 104
1212chain 'B' and (resid 105 through 237 )BAA105 - 237105 - 232
1313chain 'B' and (resid 238 through 498 )BAA238 - 498233 - 493
1414chain 'B' and (resid 499 through 609 )BAA499 - 609494 - 604

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