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- PDB-5g05: Cryo-EM structure of combined apo phosphorylated APC -

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Entry
Database: PDB / ID: 5g05
TitleCryo-EM structure of combined apo phosphorylated APC
Components
  • (ANAPHASE-PROMOTING COMPLEX SUBUNIT ...) x 11
  • (CELL DIVISION CYCLE PROTEIN ...Cell cycle) x 3
  • UNIDENTIFIED PEPTIDE
KeywordsCELL CYCLE / PHOSPHORYLATION / MITOSIS / UBIQUITINATION
Function / homology
Function and homology information


regulation of mitotic cell cycle spindle assembly checkpoint / Antigen processing: Ubiquitination & Proteasome degradation / positive regulation of synapse maturation / Conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase / Inactivation of APC/C via direct inhibition of the APC/C complex / APC/C:Cdc20 mediated degradation of mitotic proteins / anaphase-promoting complex / Aberrant regulation of mitotic exit in cancer due to RB1 defects / anaphase-promoting complex-dependent catabolic process / regulation of meiotic cell cycle ...regulation of mitotic cell cycle spindle assembly checkpoint / Antigen processing: Ubiquitination & Proteasome degradation / positive regulation of synapse maturation / Conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase / Inactivation of APC/C via direct inhibition of the APC/C complex / APC/C:Cdc20 mediated degradation of mitotic proteins / anaphase-promoting complex / Aberrant regulation of mitotic exit in cancer due to RB1 defects / anaphase-promoting complex-dependent catabolic process / regulation of meiotic cell cycle / positive regulation of mitotic metaphase/anaphase transition / metaphase/anaphase transition of mitotic cell cycle / regulation of exit from mitosis / positive regulation of synaptic plasticity / Phosphorylation of the APC/C / protein K11-linked ubiquitination / enzyme-substrate adaptor activity / regulation of mitotic metaphase/anaphase transition / positive regulation of dendrite morphogenesis / ubiquitin-ubiquitin ligase activity / mitotic metaphase chromosome alignment / regulation of mitotic cell cycle / cullin family protein binding / Regulation of APC/C activators between G1/S and early anaphase / Transcriptional Regulation by VENTX / positive regulation of axon extension / heterochromatin / APC/C:Cdc20 mediated degradation of Cyclin B / APC-Cdc20 mediated degradation of Nek2A / nuclear periphery / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / Assembly of the pre-replicative complex / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / brain development / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / mitotic spindle / spindle / kinetochore / CDK-mediated phosphorylation and removal of Cdc6 / ubiquitin-protein transferase activity / Separation of Sister Chromatids / ubiquitin protein ligase activity / microtubule cytoskeleton / Antigen processing: Ubiquitination & Proteasome degradation / mitotic cell cycle / nervous system development / ubiquitin-dependent protein catabolic process / Senescence-Associated Secretory Phenotype (SASP) / protein phosphatase binding / cell differentiation / molecular adaptor activity / protein ubiquitination / cell cycle / cell division / negative regulation of gene expression / centrosome / ubiquitin protein ligase binding / nucleolus / zinc ion binding / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
: / Anaphase-promoting complex subunit 15 / Anaphase-promoting complex subunit 15 / Anaphase-promoting complex subunit 4, metazoa / : / Anaphase-promoting complex subunit 5, N-terminal domain / Anaphase-promoting complex subunit 1, C-terminal / Anaphase-promoting complex subunit 1, middle domain / : / : ...: / Anaphase-promoting complex subunit 15 / Anaphase-promoting complex subunit 15 / Anaphase-promoting complex subunit 4, metazoa / : / Anaphase-promoting complex subunit 5, N-terminal domain / Anaphase-promoting complex subunit 1, C-terminal / Anaphase-promoting complex subunit 1, middle domain / : / : / Anaphase-promoting complex subunit 1 WD40 beta-propeller domain / Anaphase-promoting complex sub unit 1 C-terminal domain / Anaphase-promoting complex subunit 1 middle domain / APC1 beta sandwich domain / Anaphase-promoting complex subunit 16 / Anaphase-promoting complex, subunit 16 / Cdc23 / Apc13 / Anaphase-promoting complex subunit 4 / Anaphase-promoting complex subunit 4 long domain / Anaphase promoting complex subunit 8 / Cdc23 / Apc13p protein / Anaphase-promoting complex, cyclosome, subunit 4 / Anaphase-promoting complex subunit 1 / Anaphase-promoting complex subunit 5 domain / Anaphase-promoting complex subunit 5 / Anaphase-promoting complex subunit 5 / Anaphase-promoting complex subunit APC10/Doc1 / Anaphase-promoting complex, subunit CDC26 / Anaphase-promoting complex APC subunit CDC26 / Anaphase-promoting complex subunit 11, RING-H2 finger / Anaphase-promoting complex subunit 11 RING-H2 finger / Anaphase-promoting complex subunit 2, C-terminal / Anaphase-promoting complex subunit 2 / Anaphase promoting complex (APC) subunit 2 / Anaphase promoting complex (APC) subunit 2 / Anaphase-promoting complex, cyclosome, subunit 3 / APC10/DOC domain / Anaphase-promoting complex, subunit 10 (APC10) / DOC domain profile. / Anaphase-promoting complex, subunit 10 (APC10) / TPR repeat / Tetratricopeptide repeat / Anaphase-promoting complex subunit 4, WD40 domain / Anaphase-promoting complex subunit 4 WD40 domain / Tetratricopeptide repeat / Cullin / Cullin, N-terminal / Cullin homology domain / Cullin homology domain superfamily / Cullin family / Cullin family profile. / Tetratricopeptide repeat 1 / Tetratricopeptide repeat / Tetratricopeptide repeat domain / Tetratricopeptide repeat / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Galactose-binding domain-like / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Galactose-binding-like domain superfamily / Zinc finger RING-type profile. / Zinc finger, RING-type / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Armadillo-like helical / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Zinc finger, RING/FYVE/PHD-type / Winged helix DNA-binding domain superfamily / WD40-repeat-containing domain superfamily / Jelly Rolls / WD40/YVTN repeat-like-containing domain superfamily / Winged helix-like DNA-binding domain superfamily / Sandwich / 2-Layer Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Cell division cycle protein 27 homolog / Anaphase-promoting complex subunit 15 / Cell division cycle protein 16 homolog / Anaphase-promoting complex subunit 13 / Anaphase-promoting complex subunit CDC26 / Anaphase-promoting complex subunit 16 / Anaphase-promoting complex subunit 1 / Anaphase-promoting complex subunit 11 / Cell division cycle protein 23 homolog / Anaphase-promoting complex subunit 7 ...Cell division cycle protein 27 homolog / Anaphase-promoting complex subunit 15 / Cell division cycle protein 16 homolog / Anaphase-promoting complex subunit 13 / Anaphase-promoting complex subunit CDC26 / Anaphase-promoting complex subunit 16 / Anaphase-promoting complex subunit 1 / Anaphase-promoting complex subunit 11 / Cell division cycle protein 23 homolog / Anaphase-promoting complex subunit 7 / Anaphase-promoting complex subunit 5 / Anaphase-promoting complex subunit 4 / Anaphase-promoting complex subunit 2 / Anaphase-promoting complex subunit 10
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
BOS TAURUS (cattle)
UNIDENTIFIED (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsZhang, S. / Chang, L. / Alfieri, C. / Zhang, Z. / Yang, J. / Maslen, S. / Skehel, M. / Barford, D.
CitationJournal: Nature / Year: 2016
Title: Molecular mechanism of APC/C activation by mitotic phosphorylation.
Authors: Suyang Zhang / Leifu Chang / Claudio Alfieri / Ziguo Zhang / Jing Yang / Sarah Maslen / Mark Skehel / David Barford /
Abstract: In eukaryotes, the anaphase-promoting complex (APC/C, also known as the cyclosome) regulates the ubiquitin-dependent proteolysis of specific cell-cycle proteins to coordinate chromosome segregation ...In eukaryotes, the anaphase-promoting complex (APC/C, also known as the cyclosome) regulates the ubiquitin-dependent proteolysis of specific cell-cycle proteins to coordinate chromosome segregation in mitosis and entry into the G1 phase. The catalytic activity of the APC/C and its ability to specify the destruction of particular proteins at different phases of the cell cycle are controlled by its interaction with two structurally related coactivator subunits, Cdc20 and Cdh1. Coactivators recognize substrate degrons, and enhance the affinity of the APC/C for its cognate E2 (refs 4-6). During mitosis, cyclin-dependent kinase (Cdk) and polo-like kinase (Plk) control Cdc20- and Cdh1-mediated activation of the APC/C. Hyperphosphorylation of APC/C subunits, notably Apc1 and Apc3, is required for Cdc20 to activate the APC/C, whereas phosphorylation of Cdh1 prevents its association with the APC/C. Since both coactivators associate with the APC/C through their common C-box and Ile-Arg tail motifs, the mechanism underlying this differential regulation is unclear, as is the role of specific APC/C phosphorylation sites. Here, using cryo-electron microscopy and biochemical analysis, we define the molecular basis of how phosphorylation of human APC/C allows for its control by Cdc20. An auto-inhibitory segment of Apc1 acts as a molecular switch that in apo unphosphorylated APC/C interacts with the C-box binding site and obstructs engagement of Cdc20. Phosphorylation of the auto-inhibitory segment displaces it from the C-box-binding site. Efficient phosphorylation of the auto-inhibitory segment, and thus relief of auto-inhibition, requires the recruitment of Cdk-cyclin in complex with a Cdk regulatory subunit (Cks) to a hyperphosphorylated loop of Apc3. We also find that the small-molecule inhibitor, tosyl-l-arginine methyl ester, preferentially suppresses APC/C(Cdc20) rather than APC/C(Cdh1), and interacts with the binding sites of both the C-box and Ile-Arg tail motifs. Our results reveal the mechanism for the regulation of mitotic APC/C by phosphorylation and provide a rationale for the development of selective inhibitors of this state.
History
DepositionMar 16, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 25, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 8, 2016Group: Other / Refinement description
Revision 2.0Sep 11, 2019Group: Advisory / Atomic model / Data collection
Category: atom_site / em_image_scans / pdbx_unobs_or_zero_occ_atoms
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id

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Structure visualization

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Assembly

Deposited unit
A: ANAPHASE-PROMOTING COMPLEX SUBUNIT 1
B: ANAPHASE-PROMOTING COMPLEX SUBUNIT 11
C: CELL DIVISION CYCLE PROTEIN 23 HOMOLOG
D: ANAPHASE-PROMOTING COMPLEX SUBUNIT 15
E: ANAPHASE-PROMOTING COMPLEX SUBUNIT 16
F: CELL DIVISION CYCLE PROTEIN 27 HOMOLOG
G: ANAPHASE-PROMOTING COMPLEX SUBUNIT CDC26
H: CELL DIVISION CYCLE PROTEIN 27 HOMOLOG
I: ANAPHASE-PROMOTING COMPLEX SUBUNIT 4
J: CELL DIVISION CYCLE PROTEIN 16 HOMOLOG
K: CELL DIVISION CYCLE PROTEIN 16 HOMOLOG
L: ANAPHASE-PROMOTING COMPLEX SUBUNIT 10
M: ANAPHASE-PROMOTING COMPLEX SUBUNIT 13
N: ANAPHASE-PROMOTING COMPLEX SUBUNIT 2
O: ANAPHASE-PROMOTING COMPLEX SUBUNIT 5
P: CELL DIVISION CYCLE PROTEIN 23 HOMOLOG
T: UNIDENTIFIED PEPTIDE
W: ANAPHASE-PROMOTING COMPLEX SUBUNIT CDC26
X: ANAPHASE-PROMOTING COMPLEX SUBUNIT 7
Y: ANAPHASE-PROMOTING COMPLEX SUBUNIT 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,173,80323
Polymers1,173,60720
Non-polymers1963
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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ANAPHASE-PROMOTING COMPLEX SUBUNIT ... , 11 types, 13 molecules ABDEGWILMNOXY

#1: Protein ANAPHASE-PROMOTING COMPLEX SUBUNIT 1 / / APC1 / CYCLOSOME SUBUNIT 1 / MITOTIC CHECKPOINT REGULATOR / TESTIS-SPECIFIC GENE 24 PROTEIN


Mass: 216725.469 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Gene: ANAPC1, TSG24 / Plasmid: PF1, PU1 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: Q9H1A4
#2: Protein ANAPHASE-PROMOTING COMPLEX SUBUNIT 11 / / APC11 / CYCLOSOME SUBUNIT 11 / HEPATOCELLULAR CARCINOMA-ASSOCIATED RING FINGER PROTEIN


Mass: 9854.647 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Gene: ANAPC11, HSPC214 / Plasmid: PF1, PU1 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: Q9NYG5
#4: Protein ANAPHASE-PROMOTING COMPLEX SUBUNIT 15 / / APC15


Mass: 14286.727 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Gene: ANAPC15, C11ORF51, HSPC020 / Plasmid: PF1, PU1 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: P60006
#5: Protein ANAPHASE-PROMOTING COMPLEX SUBUNIT 16 / / APC16 / CYCLOSOME SUBUNIT 16


Mass: 11677.995 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Gene: ANAPC16, C10ORF104 / Plasmid: PF1, PU1 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: Q96DE5
#7: Protein ANAPHASE-PROMOTING COMPLEX SUBUNIT CDC26 / / ANAPHASE-PROMOTING COMPLEX SUBUNIT 12 / APC12 / CELL DIVISION CYCLE PROTEIN 26 HOMOLOG


Mass: 9793.999 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Gene: CDC26, ANAPC12, C9ORF17 / Plasmid: PF1, PU1 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: Q8NHZ8
#8: Protein ANAPHASE-PROMOTING COMPLEX SUBUNIT 4 / / APC4 / CYCLOSOME SUBUNIT 4


Mass: 92219.227 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Gene: ANAPC4, APC4 / Plasmid: PF1, PU1 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: Q9UJX5
#10: Protein ANAPHASE-PROMOTING COMPLEX SUBUNIT 10 / / APC10 / CYCLOSOME SUBUNIT 10


Mass: 21282.143 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Gene: ANAPC10, APC10 / Plasmid: PF1, PU1 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: Q9UM13
#11: Protein ANAPHASE-PROMOTING COMPLEX SUBUNIT 13 / / APC13 / CYCLOSOME SUBUNIT 13


Mass: 8528.309 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BOS TAURUS (cattle) / Gene: ANAPC13 / Plasmid: PF1, PU1 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: Q2NKV2
#12: Protein ANAPHASE-PROMOTING COMPLEX SUBUNIT 2 / / APC2 / CYCLOSOME SUBUNIT 2


Mass: 93938.977 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Gene: ANAPC2, APC2, KIAA1406 / Plasmid: PF1, PU1 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: Q9UJX6
#13: Protein ANAPHASE-PROMOTING COMPLEX SUBUNIT 5 / / APC5 / CYCLOSOME SUBUNIT 5


Mass: 85179.766 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Gene: ANAPC5, APC5 / Plasmid: PF1, PU1 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: Q9UJX4
#15: Protein ANAPHASE-PROMOTING COMPLEX SUBUNIT 7 / / APC7 / CYCLOSOME SUBUNIT 7


Mass: 66929.367 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Gene: ANAPC7, APC7 / Plasmid: PF1, PU1 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: Q9UJX3

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CELL DIVISION CYCLE PROTEIN ... , 3 types, 6 molecules CPFHJK

#3: Protein CELL DIVISION CYCLE PROTEIN 23 HOMOLOG / Cell cycle / ANAPHASE-PROMOTING COMPLEX SUBUNIT 8 / APC8 / CYCLOSOME SUBUNIT 8


Mass: 68921.031 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Gene: CDC23, ANAPC8 / Plasmid: PF1, PU1 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: Q9UJX2
#6: Protein CELL DIVISION CYCLE PROTEIN 27 HOMOLOG / Cell cycle / ANAPHASE-PROMOTING COMPLEX SUBUNIT 3 / APC3 / CDC27 HOMOLOG / CDC27HS / H-NUC


Mass: 91973.125 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Gene: CDC27, ANAPC3, D0S1430E, D17S978E / Plasmid: PF1, PU1 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: P30260
#9: Protein CELL DIVISION CYCLE PROTEIN 16 HOMOLOG / Cell cycle / ANAPHASE-PROMOTING COMPLEX SUBUNIT 6 / APC6 / CDC16 HOMOLOG / CDC16HS / CYCLOSOME SUBUNIT 6


Mass: 71747.516 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Gene: CDC16, ANAPC6 / Plasmid: PF1, PU1 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: Q13042

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Protein/peptide / Non-polymers , 2 types, 4 molecules T

#14: Protein/peptide UNIDENTIFIED PEPTIDE


Mass: 1183.313 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) UNIDENTIFIED (others) / Plasmid: PF1, PU1 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm)
#16: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: RECOMBINANT APO PHOSPHORYLATED APC / Type: COMPLEX
Buffer solutionName: 20MM HEPES, 150MM NACL, 0. 5MM TCEP / pH: 8 / Details: 20MM HEPES, 150MM NACL, 0. 5MM TCEP
SpecimenConc.: 0.15 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: CARBON
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Details: LIQUID ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300 / Date: Oct 1, 2015
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 78000 X / Nominal defocus max: 4000 nm / Nominal defocus min: 2000 nm / Cs: 2 mm
Specimen holderTemperature: 105 K
Image recordingElectron dose: 27 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 921993 / Refinement type: HALF-MAPS REFINED INDEPENDENTLY / Symmetry type: POINT
RefinementHighest resolution: 3.5 Å
Refinement stepCycle: LAST / Highest resolution: 3.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms63173 0 3 0 63176

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