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- PDB-6c9j: AMP-activated protein kinase bound to pharmacological activator R734 -

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Basic information

Entry
Database: PDB / ID: 6c9j
TitleAMP-activated protein kinase bound to pharmacological activator R734
Components
  • (5'-AMP-activated protein kinase subunit ...) x 2
  • 5'-AMP-activated protein kinase catalytic subunit alpha-1
KeywordsTRANSFERASE / AMPK / activator
Function / homology
Function and homology information


negative regulation of glucosylceramide biosynthetic process / positive regulation of peptidyl-lysine acetylation / positive regulation of mitochondrial transcription / [hydroxymethylglutaryl-CoA reductase (NADPH)] kinase / nail development / [hydroxymethylglutaryl-CoA reductase (NADPH)] kinase activity / regulation of stress granule assembly / cold acclimation / cAMP-dependent protein kinase regulator activity / lipid droplet disassembly ...negative regulation of glucosylceramide biosynthetic process / positive regulation of peptidyl-lysine acetylation / positive regulation of mitochondrial transcription / [hydroxymethylglutaryl-CoA reductase (NADPH)] kinase / nail development / [hydroxymethylglutaryl-CoA reductase (NADPH)] kinase activity / regulation of stress granule assembly / cold acclimation / cAMP-dependent protein kinase regulator activity / lipid droplet disassembly / Lipophagy / regulation of carbon utilization / positive regulation of skeletal muscle tissue development / CAMKK-AMPK signaling cascade / import into nucleus / regulation of vesicle-mediated transport / nucleotide-activated protein kinase complex / Energy dependent regulation of mTOR by LKB1-AMPK / positive regulation of T cell mediated immune response to tumor cell / tau-protein kinase / negative regulation of hepatocyte apoptotic process / cellular response to ethanol / protein kinase regulator activity / negative regulation of TOR signaling / Activation of PPARGC1A (PGC-1alpha) by phosphorylation / response to caffeine / positive regulation of protein targeting to mitochondrion / regulation of glycolytic process / cAMP-dependent protein kinase activity / protein localization to lipid droplet / motor behavior / tau-protein kinase activity / lipid biosynthetic process / negative regulation of tubulin deacetylation / Macroautophagy / cellular response to stress / cholesterol biosynthetic process / AMP binding / fatty acid oxidation / positive regulation of protein kinase activity / fatty acid homeostasis / cellular response to nutrient levels / negative regulation of lipid catabolic process / response to UV / cellular response to glucose starvation / Activation of AMPK downstream of NMDARs / energy homeostasis / positive regulation of protein localization / positive regulation of adipose tissue development / negative regulation of TORC1 signaling / positive regulation of autophagy / positive regulation of gluconeogenesis / negative regulation of insulin receptor signaling pathway / regulation of microtubule cytoskeleton organization / cellular response to calcium ion / positive regulation of glycolytic process / response to activity / response to gamma radiation / Translocation of SLC2A4 (GLUT4) to the plasma membrane / TP53 Regulates Metabolic Genes / positive regulation of cholesterol biosynthetic process / cellular response to glucose stimulus / regulation of circadian rhythm / ADP binding / tau protein binding / autophagy / positive regulation of T cell activation / cellular response to hydrogen peroxide / Wnt signaling pathway / neuron cellular homeostasis / response to estrogen / glucose metabolic process / fatty acid biosynthetic process / rhythmic process / cellular response to prostaglandin E stimulus / glucose homeostasis / cellular response to xenobiotic stimulus / positive regulation of cold-induced thermogenesis / cellular response to oxidative stress / spermatogenesis / cellular response to hypoxia / Regulation of TP53 Activity through Phosphorylation / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity
Similarity search - Function
PRKAA1, UBA-like autoinhibitory domain / 5'-AMP-activated protein kinase alpha 1 catalytic subunit, C-terminal / : / AMP-activated protein kinase, alpha subunit, autoinhibitory domain / : / Association with the SNF1 complex (ASC) domain / ASC domain superfamily / : / 5'-AMP-activated protein kinase beta subunit, interaction domain / 5'-AMP-activated protein kinase beta subunit, interation domain ...PRKAA1, UBA-like autoinhibitory domain / 5'-AMP-activated protein kinase alpha 1 catalytic subunit, C-terminal / : / AMP-activated protein kinase, alpha subunit, autoinhibitory domain / : / Association with the SNF1 complex (ASC) domain / ASC domain superfamily / : / 5'-AMP-activated protein kinase beta subunit, interaction domain / 5'-AMP-activated protein kinase beta subunit, interation domain / AMPK, C-terminal adenylate sensor domain / Adenylate sensor of SNF1-like protein kinase / AMP-activated protein kinase, glycogen-binding domain / Glycogen recognition site of AMP-activated protein kinase / KA1 domain/Ssp2, C-terminal / Domain in cystathionine beta-synthase and other proteins. / CBS domain superfamily / CBS domain / CBS domain / CBS domain profile. / Immunoglobulin E-set / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / Chem-R34 / STAUROSPORINE / 5'-AMP-activated protein kinase subunit gamma-1 / 5'-AMP-activated protein kinase catalytic subunit alpha-1 / 5'-AMP-activated protein kinase subunit beta-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.05 Å
AuthorsYan, Y. / Zhou, X.E. / Novick, S. / Shaw, S.J. / Li, Y. / Brunzelle, J.S. / Hitoshi, Y. / Griffin, P.R. / Xu, H.E. / Melcher, K.
Funding support United States, China, 8items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)GM102545 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)DK071662 United States
National Natural Science Foundation of China (NSFC)31300245 China
Ministry of Science and Technology (MoST, China)2012ZX09301001 China
Ministry of Science and Technology (MoST, China)2012CB910403 China
Ministry of Science and Technology (MoST, China)2013CB910600 China
Ministry of Science and Technology (MoST, China)XDB08020303 China
Ministry of Science and Technology (MoST, China)2013ZX09507001 China
CitationJournal: J. Biol. Chem. / Year: 2019
Title: Structures of AMP-activated protein kinase bound to novel pharmacological activators in phosphorylated, non-phosphorylated, and nucleotide-free states.
Authors: Yan, Y. / Zhou, X.E. / Novick, S.J. / Shaw, S.J. / Li, Y. / Brunzelle, J.S. / Hitoshi, Y. / Griffin, P.R. / Xu, H.E. / Melcher, K.
History
DepositionJan 26, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 28, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 12, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 30, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: 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
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 5'-AMP-activated protein kinase catalytic subunit alpha-1
B: 5'-AMP-activated protein kinase subunit beta-1
C: 5'-AMP-activated protein kinase subunit gamma-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,6056
Polymers117,3453
Non-polymers1,2613
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13240 Å2
ΔGint-73 kcal/mol
Surface area39930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.296, 123.296, 404.921
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

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Protein , 1 types, 1 molecules A

#1: Protein 5'-AMP-activated protein kinase catalytic subunit alpha-1 / AMPK subunit alpha-1 / Acetyl-CoA carboxylase kinase / ACACA kinase / Hydroxymethylglutaryl-CoA ...AMPK subunit alpha-1 / Acetyl-CoA carboxylase kinase / ACACA kinase / Hydroxymethylglutaryl-CoA reductase kinase / HMGCR kinase / Tau-protein kinase PRKAA1


Mass: 57245.625 Da / Num. of mol.: 1 / Mutation: S108D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRKAA1, AMPK1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q13131, non-specific serine/threonine protein kinase, EC: 2.7.11.27, [hydroxymethylglutaryl-CoA reductase (NADPH)] kinase, tau-protein kinase

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5'-AMP-activated protein kinase subunit ... , 2 types, 2 molecules BC

#2: Protein 5'-AMP-activated protein kinase subunit beta-1 / AMPKb


Mass: 23071.316 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRKAB1, AMPK / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y478
#3: Protein 5'-AMP-activated protein kinase subunit gamma-1 / AMPKg


Mass: 37027.598 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRKAG1 / Production host: Escherichia coli (E. coli) / References: UniProt: P54619

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Non-polymers , 3 types, 3 molecules

#4: Chemical ChemComp-R34 / 5-{[6-chloro-5-(1-methyl-1H-indol-5-yl)-1H-benzimidazol-2-yl]oxy}-N-hydroxy-2-methylbenzamide


Mass: 446.886 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H19ClN4O3
#5: Chemical ChemComp-STU / STAUROSPORINE


Mass: 466.531 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H26N4O3 / Comment: anticancer, antifungal, antibiotic, alkaloid*YM
#6: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM

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Details

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: 3.77 Å3/Da / Density % sol: 67.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 0.1 M tri-ammonium citrate pH7, 12% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 11, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.05→50 Å / Num. obs: 32841 / % possible obs: 91.1 % / Redundancy: 34.4 % / CC1/2: 0.997 / Rmerge(I) obs: 0.807 / Net I/σ(I): 10
Reflection shellResolution: 3.05→3.22 Å / Rmerge(I) obs: 0.0897 / CC1/2: 0.722

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4RER

4rer


Resolution: 3.05→49.646 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2246 2366 7.24 %
Rwork0.2144 --
obs0.2151 32702 91.34 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.05→49.646 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6944 0 90 0 7034
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0047211
X-RAY DIFFRACTIONf_angle_d0.7829796
X-RAY DIFFRACTIONf_dihedral_angle_d9.5314308
X-RAY DIFFRACTIONf_chiral_restr0.0531104
X-RAY DIFFRACTIONf_plane_restr0.0061218
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0501-3.11230.3893920.36441048X-RAY DIFFRACTION55
3.1123-3.180.2641890.32661122X-RAY DIFFRACTION59
3.18-3.25390.29551040.31561265X-RAY DIFFRACTION66
3.2539-3.33530.3761940.28921457X-RAY DIFFRACTION75
3.3353-3.42550.24221250.27561835X-RAY DIFFRACTION95
3.4255-3.52620.27051460.25661912X-RAY DIFFRACTION100
3.5262-3.640.23271530.24111908X-RAY DIFFRACTION100
3.64-3.77010.24361370.24011922X-RAY DIFFRACTION100
3.7701-3.9210.22031390.21221940X-RAY DIFFRACTION100
3.921-4.09930.23071640.20651931X-RAY DIFFRACTION100
4.0993-4.31530.21821600.19141916X-RAY DIFFRACTION100
4.3153-4.58550.2131610.17991940X-RAY DIFFRACTION100
4.5855-4.93930.18251520.18581971X-RAY DIFFRACTION100
4.9393-5.43580.21651550.19021961X-RAY DIFFRACTION100
5.4358-6.22110.20911590.21561999X-RAY DIFFRACTION100
6.2211-7.83290.21541790.21232016X-RAY DIFFRACTION100
7.8329-49.65250.19681570.18462193X-RAY DIFFRACTION99
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)
13.40751.41531.36792.6043-0.03443.3250.02320.24480.129-0.10520.0877-0.0958-0.21110.1166-0.11090.5313-0.0018-0.00320.4342-0.11050.4644-9.408726.6555-32.2436
23.5482-0.91951.53760.6874-0.16742.3805-0.0054-0.08290.1498-0.04190.01560.1866-0.4875-0.3542-0.01020.6193-0.03390.02960.5275-0.04620.5061-23.126436.2116-30.5525
30.54810.1988-0.30990.7438-0.41520.9594-0.0125-0.01780.03620.0108-0.0036-0.0426-0.1251-0.03280.01610.4520.0315-0.03580.3911-0.11450.412-19.564325.0595-16.4564
41.07960.5547-0.13463.61021.17991.0679-0.03560.05940.1688-0.1362-0.00870.2391-0.2442-0.21110.04430.65930.0732-0.04420.6276-0.09930.5693-38.693730.7522-17.6189
50.8918-0.26520.21990.8845-0.01910.97830.0050.0212-0.1067-0.07820.00710.17310.0248-0.2524-0.01210.45210.0454-0.01890.4497-0.1090.4318-35.890114.8371-9.0951
60.8216-0.5539-0.68020.37340.45860.56320.0611-0.44010.52920.22040.0995-0.0326-0.3743-0.0883-0.16060.7240.0484-0.02420.6586-0.08880.678-32.215933.09365.2525
70.3768-0.30420.38090.31520.07992.5430.14070.28910.0841-0.4095-0.09990.0746-0.2087-0.0308-0.04081.30720.4285-0.03131.1343-0.16651.0946-52.489951.5232-15.9957
82.6995-0.3451-0.12051.9502-0.30433.1018-0.0189-0.13240.19650.1669-0.0626-0.0467-0.23780.03130.08150.5478-0.11350.00650.4651-0.10130.4566-10.976532.2015-52.1563
90000000.0478-0.05610.31080.07440.02530.2347-0.2198-0.2286-0.07311.00830.05210.00440.9866-0.05481.0523-30.755944.7066-35.7549
100000000.2109-0.54480.12020.7382-0.0158-0.38410.32260.1666-0.1951.15920.34930.1221.1807-0.17661.1278-43.460143.24114.5662
110.37310.2305-0.13731.98360.29931.87920.0073-0.07350.02060.0437-0.01310.0212-0.0643-0.050.00590.9340.32820.13360.9144-0.14990.88-44.835951.0542-3.126
121.63360.86330.35130.45620.18560.0755-0.0021-0.20450.15850.1968-0.0496-0.3844-0.28460.35530.05170.97570.11350.10851.0455-0.1011.1737-24.17759.91915.638
130.304-0.3161-0.82340.55880.8252.23430.01290.2138-0.0001-0.2352-0.0369-0.0628-0.0926-0.08050.02410.85430.22910.19180.7643-0.07330.9301-52.984367.76019.0558
144.9417-1.4233-1.82970.40990.5270.67750.0169-0.03660.6901-0.00860.2096-0.594-0.29860.3595-0.22661.19770.18340.1641.2983-0.15551.4145-43.06774.68013.517
150.8320.52440.84620.33050.53330.8606-0.0229-0.06680.24630.0839-0.005-0.343-0.22840.28050.02791.07450.1080.16611.2542-0.1781.4571-30.352170.08027.6699
162.6727-0.11322.09192.5088-0.80275.63620.10240.0481-0.02370.0867-0.1072-0.31560.310.42370.00480.91440.10530.20481.11-0.18991.3293-29.306959.78826.4643
17000000-0.03030.05270.0148-0.04610.0294-0.23180.05130.14640.00091.57310.09520.13011.762-0.20341.9939-13.999464.726422.9805
182.5609-0.37740.12061.29710.86870.63870.0422-0.21410.1190.2174-0.0373-0.4611-0.16850.4279-0.00490.85570.16240.070.9624-0.10061.0644-41.131673.026730.278
191.14070.07110.5061.4410.73512.45330.0728-0.1192-0.35290.154-0.0151-0.17290.30840.1174-0.05770.71510.19810.06850.7824-0.03130.8518-50.285562.764326.263
200.5452-0.23750.93740.1035-0.40841.61170.1473-0.1465-0.33710.07490.02820.00050.2025-0.2144-0.17551.58850.08230.09171.7172-0.23421.826-32.428259.451732.585
211.7118-0.2999-0.3390.9555-0.49740.83790.007-0.1104-0.03720.17950.0578-0.13050.18050.1754-0.06481.20620.05350.06691.333-0.23711.4721-28.118962.200329.1838
222.94320.96331.60242.96480.04980.9574-0.00420.45180.0391-0.35420.0766-0.2693-0.12830.0345-0.07241.18090.07070.06181.2919-0.2461.4525-25.435170.345921.503
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 11 through 42 )
2X-RAY DIFFRACTION2chain 'A' and (resid 43 through 72 )
3X-RAY DIFFRACTION3chain 'A' and (resid 73 through 162 )
4X-RAY DIFFRACTION4chain 'A' and (resid 163 through 194 )
5X-RAY DIFFRACTION5chain 'A' and (resid 195 through 250 )
6X-RAY DIFFRACTION6chain 'A' and (resid 251 through 370 )
7X-RAY DIFFRACTION7chain 'A' and (resid 371 through 550 )
8X-RAY DIFFRACTION8chain 'B' and (resid 74 through 148 )
9X-RAY DIFFRACTION9chain 'B' and (resid 149 through 207 )
10X-RAY DIFFRACTION10chain 'B' and (resid 208 through 226 )
11X-RAY DIFFRACTION11chain 'B' and (resid 227 through 270 )
12X-RAY DIFFRACTION12chain 'C' and (resid 25 through 48 )
13X-RAY DIFFRACTION13chain 'C' and (resid 49 through 112 )
14X-RAY DIFFRACTION14chain 'C' and (resid 113 through 136 )
15X-RAY DIFFRACTION15chain 'C' and (resid 137 through 155 )
16X-RAY DIFFRACTION16chain 'C' and (resid 156 through 179 )
17X-RAY DIFFRACTION17chain 'C' and (resid 180 through 195 )
18X-RAY DIFFRACTION18chain 'C' and (resid 196 through 235 )
19X-RAY DIFFRACTION19chain 'C' and (resid 236 through 268 )
20X-RAY DIFFRACTION20chain 'C' and (resid 269 through 283 )
21X-RAY DIFFRACTION21chain 'C' and (resid 284 through 307 )
22X-RAY DIFFRACTION22chain 'C' and (resid 308 through 324 )

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