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- PDB-9fmm: Structure of human ACE2 in complex with a fluorinated small molec... -

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Basic information

Entry
Database: PDB / ID: 9fmm
TitleStructure of human ACE2 in complex with a fluorinated small molecule inhibitor
ComponentsAngiotensin-converting enzyme 2
KeywordsPEPTIDE BINDING PROTEIN / Enzyme / peptidase / SARS-CoV-2 receptor / renin-angiotensin-aldosterone system
Function / homology
Function and homology information


positive regulation of amino acid transport / angiotensin-converting enzyme 2 / positive regulation of L-proline import across plasma membrane / Hydrolases; Acting on peptide bonds (peptidases); Metallocarboxypeptidases / angiotensin-mediated drinking behavior / regulation of systemic arterial blood pressure by renin-angiotensin / tryptophan transport / positive regulation of gap junction assembly / regulation of vasoconstriction / regulation of cardiac conduction ...positive regulation of amino acid transport / angiotensin-converting enzyme 2 / positive regulation of L-proline import across plasma membrane / Hydrolases; Acting on peptide bonds (peptidases); Metallocarboxypeptidases / angiotensin-mediated drinking behavior / regulation of systemic arterial blood pressure by renin-angiotensin / tryptophan transport / positive regulation of gap junction assembly / regulation of vasoconstriction / regulation of cardiac conduction / peptidyl-dipeptidase activity / maternal process involved in female pregnancy / angiotensin maturation / Metabolism of Angiotensinogen to Angiotensins / metallocarboxypeptidase activity / carboxypeptidase activity / negative regulation of signaling receptor activity / Attachment and Entry / positive regulation of cardiac muscle contraction / regulation of cytokine production / viral life cycle / blood vessel diameter maintenance / brush border membrane / regulation of transmembrane transporter activity / negative regulation of smooth muscle cell proliferation / negative regulation of ERK1 and ERK2 cascade / cilium / metallopeptidase activity / endocytic vesicle membrane / positive regulation of reactive oxygen species metabolic process / virus receptor activity / regulation of cell population proliferation / regulation of inflammatory response / endopeptidase activity / Induction of Cell-Cell Fusion / Potential therapeutics for SARS / entry receptor-mediated virion attachment to host cell / receptor-mediated endocytosis of virus by host cell / membrane fusion / Attachment and Entry / receptor-mediated virion attachment to host cell / symbiont entry into host cell / membrane raft / apical plasma membrane / endoplasmic reticulum lumen / cell surface / extracellular space / zinc ion binding / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane
Similarity search - Function
Collectrin-like domain profile. / Collectrin domain / Renal amino acid transporter / Peptidase family M2 domain profile. / Peptidase M2, peptidyl-dipeptidase A / Angiotensin-converting enzyme / Neutral zinc metallopeptidases, zinc-binding region signature.
Similarity search - Domain/homology
: / Angiotensin-converting enzyme 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsBenoit, R.B. / Rodrigues, M.J. / Wieser, M.M.
Funding support Switzerland, 3items
OrganizationGrant numberCountry
Other privatePromedica 1401/M
Swiss National Science FoundationCRSK-3_190414 Switzerland
Swiss National Science Foundation198274 Switzerland
CitationJournal: European Journal of Nuclear Medicine and Molecular Imaging
Year: 2024
Title: Development of radiofluorinated MLN-4760 derivatives for PET imaging of the SARS-CoV-2 entry receptor ACE2
Authors: Wang, J. / Beyer, D. / Vaccarin, C. / He, Y. / Tanriver, M. / Benoit, R. / Deupi, X. / Mu, L. / Bode, J.W. / Schibli, R. / Mueller, C.
History
DepositionJun 6, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 17, 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: Angiotensin-converting enzyme 2
B: Angiotensin-converting enzyme 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,31026
Polymers169,3172
Non-polymers2,99324
Water2,738152
1
A: Angiotensin-converting enzyme 2
hetero molecules


  • defined by author
  • Evidence: gel filtration, The full length protein can dimerize.
  • 86.2 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)86,16813
Polymers84,6581
Non-polymers1,51012
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Angiotensin-converting enzyme 2
hetero molecules


  • defined by author
  • 86.1 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)86,14213
Polymers84,6581
Non-polymers1,48312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)99.300, 82.900, 105.500
Angle α, β, γ (deg.)90.000, 104.200, 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

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Protein / Sugars , 2 types, 8 molecules AB

#1: Protein Angiotensin-converting enzyme 2 / Angiotensin-converting enzyme homolog / ACEH / Angiotensin-converting enzyme-related ...Angiotensin-converting enzyme homolog / ACEH / Angiotensin-converting enzyme-related carboxypeptidase / ACE-related carboxypeptidase / Metalloprotease MPROT15


Mass: 84658.445 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACE2, UNQ868/PRO1885 / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: Q9BYF1, angiotensin-converting enzyme 2, Hydrolases; Acting on peptide bonds (peptidases); Metallocarboxypeptidases
#3: 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.: 6 / 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 , 6 types, 170 molecules

#2: Chemical ChemComp-A1IDX / (2~{S})-2-[[(2~{S})-3-[3-[(3-chloranyl-5-fluoranyl-phenyl)methyl]imidazol-4-yl]-1-oxidanyl-1-oxidanylidene-propan-2-yl]amino]-4-methyl-pentanoic acid


Mass: 411.855 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H23ClFN3O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#7: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 152 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.49 Å3/Da / Density % sol: 50.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.1 M sodium citrate pH 5.5, 20% w/v PEG 3000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 2, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→48.36 Å / Num. obs: 110900 / % possible obs: 98.2 % / Redundancy: 3.58 % / CC1/2: 0.978 / Net I/σ(I): 6.52
Reflection shellResolution: 2.5→2.56 Å / Redundancy: 3.62 % / Num. unique obs: 8186 / CC1/2: 0.235 / % possible all: 97.8

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Processing

Software
NameVersionClassification
PHENIX1.20_4459refinement
PHENIX1.20_4459refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→48.36 Å / SU ML: 0.4215 / Cross valid method: FREE R-VALUE / σ(F): 0.86 / Phase error: 31.5343
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2651 5532 4.99 %
Rwork0.2126 105309 -
obs0.2152 110841 98.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 60.61 Å2
Refinement stepCycle: LAST / Resolution: 2.5→48.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11022 0 183 152 11357
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007811486
X-RAY DIFFRACTIONf_angle_d0.923115563
X-RAY DIFFRACTIONf_chiral_restr0.05351645
X-RAY DIFFRACTIONf_plane_restr0.00772006
X-RAY DIFFRACTIONf_dihedral_angle_d15.45834226
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.530.44731810.38123440X-RAY DIFFRACTION95.97
2.53-2.560.38531830.35423512X-RAY DIFFRACTION99.46
2.56-2.590.37311870.32853582X-RAY DIFFRACTION99.63
2.59-2.620.36551880.31293564X-RAY DIFFRACTION99.42
2.62-2.660.32321850.30853550X-RAY DIFFRACTION99.36
2.66-2.690.36651840.30093575X-RAY DIFFRACTION99.37
2.69-2.730.32481860.29143493X-RAY DIFFRACTION99.24
2.73-2.770.33851880.29623546X-RAY DIFFRACTION98.84
2.77-2.820.31181860.29273518X-RAY DIFFRACTION98.91
2.82-2.860.34211910.29063610X-RAY DIFFRACTION99.42
2.86-2.910.32351850.2723490X-RAY DIFFRACTION98.9
2.91-2.960.36411850.25963519X-RAY DIFFRACTION98.98
2.96-3.020.34051880.24463537X-RAY DIFFRACTION98.65
3.02-3.080.28241820.23133531X-RAY DIFFRACTION98.44
3.08-3.150.25081820.21513482X-RAY DIFFRACTION96.98
3.15-3.220.26471740.23263357X-RAY DIFFRACTION94.01
3.22-3.30.29571790.22953407X-RAY DIFFRACTION94.67
3.3-3.390.30731850.21933527X-RAY DIFFRACTION99.49
3.39-3.490.2911890.20763560X-RAY DIFFRACTION99.73
3.49-3.610.25041860.19553557X-RAY DIFFRACTION99.49
3.61-3.730.26961840.18723519X-RAY DIFFRACTION99.57
3.73-3.880.22151870.17773565X-RAY DIFFRACTION99.47
3.88-4.060.21621890.17713577X-RAY DIFFRACTION99.24
4.06-4.270.2391810.17293505X-RAY DIFFRACTION99.01
4.27-4.540.21341850.17563525X-RAY DIFFRACTION98.12
4.54-4.890.24071860.17443486X-RAY DIFFRACTION97.48
4.89-5.380.24931850.19163476X-RAY DIFFRACTION97.13
5.38-6.160.2321750.21473329X-RAY DIFFRACTION93.34
6.16-7.760.21691810.19963449X-RAY DIFFRACTION96.54
7.76-48.360.23371850.17973521X-RAY DIFFRACTION98.46

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