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- PDB-8toq: ACE2-peptide 1 complex -

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Basic information

Entry
Database: PDB / ID: 8toq
TitleACE2-peptide 1 complex
Components
  • Angiotensin-converting enzyme 2
  • Peptide 1
KeywordsPROTEIN BINDING / Peptidase / enzyme / complex / SARS-CoV-2 / angiotensin
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 cardiac conduction / regulation of vasoconstriction ...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 cardiac conduction / regulation of vasoconstriction / peptidyl-dipeptidase activity / maternal process involved in female pregnancy / angiotensin maturation / Metabolism of Angiotensinogen to Angiotensins / negative regulation of signaling receptor activity / carboxypeptidase activity / Attachment and Entry / positive regulation of cardiac muscle contraction / viral life cycle / regulation of cytokine production / blood vessel diameter maintenance / negative regulation of smooth muscle cell proliferation / brush border membrane / regulation of transmembrane transporter activity / cilium / negative regulation of ERK1 and ERK2 cascade / metallopeptidase activity / positive regulation of reactive oxygen species metabolic process / endocytic vesicle membrane / virus receptor activity / regulation of cell population proliferation / regulation of inflammatory response / endopeptidase activity / Potential therapeutics for SARS / Induction of Cell-Cell Fusion / entry receptor-mediated virion attachment to host cell / membrane fusion / receptor-mediated endocytosis of virus by host cell / 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 / extracellular exosome / zinc ion binding / extracellular region / identical protein binding / membrane / plasma membrane
Similarity search - Function
Collectrin domain / Renal amino acid transporter / Collectrin-like domain profile. / Peptidase M2, peptidyl-dipeptidase A / Angiotensin-converting enzyme / Peptidase family M2 domain profile. / Neutral zinc metallopeptidases, zinc-binding region signature.
Similarity search - Domain/homology
Angiotensin-converting enzyme 2
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsChristie, M. / Payne, R.J.
Funding support Australia, 4items
OrganizationGrant numberCountry
Australian Research Council (ARC)DP220102497 Australia
Australian Research Council (ARC)CE200100012 Australia
National Health and Medical Research Council (NHMRC, Australia)APP1141142 Australia
National Health and Medical Research Council (NHMRC, Australia)APP1153493 Australia
CitationJournal: Acs Chem.Biol. / Year: 2024
Title: Discovery of High Affinity Cyclic Peptide Ligands for Human ACE2 with SARS-CoV-2 Entry Inhibitory Activity.
Authors: Bedding, M.J. / Franck, C. / Johansen-Leete, J. / Aggarwal, A. / Maxwell, J.W.C. / Patel, K. / Hawkins, P.M.E. / Low, J.K.K. / Siddiquee, R. / Sani, H.M. / Ford, D.J. / Turville, S. / ...Authors: Bedding, M.J. / Franck, C. / Johansen-Leete, J. / Aggarwal, A. / Maxwell, J.W.C. / Patel, K. / Hawkins, P.M.E. / Low, J.K.K. / Siddiquee, R. / Sani, H.M. / Ford, D.J. / Turville, S. / Mackay, J.P. / Passioura, T. / Christie, M. / Payne, R.J.
History
DepositionAug 3, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 7, 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
E: Peptide 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,9847
Polymers74,2192
Non-polymers7645
Water2,630146
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2930 Å2
ΔGint-47 kcal/mol
Surface area25930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)180.281, 180.281, 71.646
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Space group name HallR3
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x+1/3,y+2/3,z+2/3
#5: -y+1/3,x-y+2/3,z+2/3
#6: -x+y+1/3,-x+2/3,z+2/3
#7: x+2/3,y+1/3,z+1/3
#8: -y+2/3,x-y+1/3,z+1/3
#9: -x+y+2/3,-x+1/3,z+1/3

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Components

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Protein / Protein/peptide / Sugars , 3 types, 5 molecules AE

#1: Protein Angiotensin-converting enzyme 2


Mass: 72592.398 Da / Num. of mol.: 1 / Fragment: protease domain
Source method: isolated from a genetically manipulated source
Details: ACE2 protease domain with C-terminal His-Avi tag / Source: (gene. exp.) Homo sapiens (human) / Gene: ACE2 / Production host: Homo sapiens (human) / References: UniProt: Q9BYF1
#2: Protein/peptide Peptide 1


Mass: 1626.986 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic cyclic peptide / Source: (synth.) synthetic construct (others)
#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.: 3 / 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 , 3 types, 148 molecules

#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 3.19 Å3/Da / Density % sol: 61.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG5KMME, magnesium formate, sodium acetate 4.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 12, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.3→45.55 Å / Num. obs: 38423 / % possible obs: 99.8 % / Redundancy: 10.8 % / Biso Wilson estimate: 39.4 Å2 / CC1/2: 0.998 / Net I/σ(I): 10.2
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 10.8 % / Num. unique obs: 3733 / CC1/2: 0.86 / % possible all: 98

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→45.55 Å / SU ML: 0.2808 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 24.3075
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2153 2021 5.26 %
Rwork0.1823 36391 -
obs0.1842 38412 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.28 Å2
Refinement stepCycle: LAST / Resolution: 2.3→45.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4940 0 47 146 5133
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00355124
X-RAY DIFFRACTIONf_angle_d0.58676960
X-RAY DIFFRACTIONf_chiral_restr0.0393734
X-RAY DIFFRACTIONf_plane_restr0.005894
X-RAY DIFFRACTIONf_dihedral_angle_d5.5073670
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.360.30571400.24292532X-RAY DIFFRACTION97.23
2.36-2.420.26771660.22072562X-RAY DIFFRACTION99.89
2.42-2.490.281100.22412650X-RAY DIFFRACTION100
2.49-2.570.29521550.21972598X-RAY DIFFRACTION99.96
2.57-2.670.25511530.21322621X-RAY DIFFRACTION99.96
2.67-2.770.26111480.20642591X-RAY DIFFRACTION100
2.77-2.90.25531490.22732579X-RAY DIFFRACTION100
2.9-3.050.25721060.2112640X-RAY DIFFRACTION100
3.05-3.240.24581270.21352639X-RAY DIFFRACTION100
3.24-3.490.25781620.19692575X-RAY DIFFRACTION100
3.49-3.850.21391550.18482606X-RAY DIFFRACTION100
3.85-4.40.17421430.14652621X-RAY DIFFRACTION100
4.4-5.540.16351620.14322571X-RAY DIFFRACTION100
5.55-45.550.16991450.15242606X-RAY DIFFRACTION99.82

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