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Yorodumi- PDB-7q28: Crystal structure of Angiotensin-1 converting enzyme C-domain in ... -
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-Basic information
Entry | Database: PDB / ID: 7q28 | ||||||
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Title | Crystal structure of Angiotensin-1 converting enzyme C-domain in complex with dual ACE/NEP inhibitor AD012 | ||||||
Components | Angiotensin-converting enzyme | ||||||
Keywords | HYDROLASE / Angiotensin-1 converting enzyme / Dual inhibitor / NEP / Metalloprotease | ||||||
Function / homology | Function and homology information mononuclear cell proliferation / cell proliferation in bone marrow / bradykinin receptor binding / regulation of angiotensin metabolic process / exopeptidase activity / substance P catabolic process / peptidyl-dipeptidase A / tripeptidyl-peptidase activity / regulation of renal output by angiotensin / negative regulation of calcium ion import ...mononuclear cell proliferation / cell proliferation in bone marrow / bradykinin receptor binding / regulation of angiotensin metabolic process / exopeptidase activity / substance P catabolic process / peptidyl-dipeptidase A / tripeptidyl-peptidase activity / regulation of renal output by angiotensin / negative regulation of calcium ion import / positive regulation of peptidyl-cysteine S-nitrosylation / response to laminar fluid shear stress / negative regulation of gap junction assembly / metallodipeptidase activity / positive regulation of systemic arterial blood pressure / cellular response to aldosterone / hormone catabolic process / bradykinin catabolic process / angiogenesis involved in coronary vascular morphogenesis / response to thyroid hormone / antigen processing and presentation of peptide antigen via MHC class I / negative regulation of glucose import / vasoconstriction / hormone metabolic process / neutrophil mediated immunity / regulation of smooth muscle cell migration / regulation of hematopoietic stem cell proliferation / mitogen-activated protein kinase binding / embryo development ending in birth or egg hatching / chloride ion binding / mitogen-activated protein kinase kinase binding / positive regulation of neurogenesis / arachidonic acid secretion / post-transcriptional regulation of gene expression / eating behavior / heterocyclic compound binding / lung alveolus development / heart contraction / peptide catabolic process / response to dexamethasone / regulation of heart rate by cardiac conduction / regulation of systemic arterial blood pressure by renin-angiotensin / regulation of vasoconstriction / peptidyl-dipeptidase activity / hematopoietic stem cell differentiation / blood vessel remodeling / angiotensin maturation / amyloid-beta metabolic process / animal organ regeneration / Metabolism of Angiotensinogen to Angiotensins / carboxypeptidase activity / positive regulation of vasoconstriction / sperm midpiece / blood vessel diameter maintenance / response to nutrient levels / basal plasma membrane / kidney development / angiotensin-activated signaling pathway / female pregnancy / cellular response to glucose stimulus / brush border membrane / regulation of synaptic plasticity / metalloendopeptidase activity / regulation of blood pressure / metallopeptidase activity / male gonad development / actin binding / peptidase activity / spermatogenesis / endopeptidase activity / response to lipopolysaccharide / lysosome / calmodulin binding / response to hypoxia / endosome / response to xenobiotic stimulus / positive regulation of apoptotic process / external side of plasma membrane / negative regulation of gene expression / proteolysis / extracellular space / zinc ion binding / extracellular exosome / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | ||||||
Authors | Cozier, G.E. / Acharya, K.R. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: J.Med.Chem. / Year: 2022 Title: Probing the Requirements for Dual Angiotensin-Converting Enzyme C-Domain Selective/Neprilysin Inhibition. Authors: Arendse, L.B. / Cozier, G.E. / Eyermann, C.J. / Basarab, G.S. / Schwager, S.L. / Chibale, K. / Acharya, K.R. / Sturrock, E.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7q28.cif.gz | 445.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7q28.ent.gz | 301.2 KB | Display | PDB format |
PDBx/mmJSON format | 7q28.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7q28_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 7q28_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 7q28_validation.xml.gz | 26.4 KB | Display | |
Data in CIF | 7q28_validation.cif.gz | 39.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q2/7q28 ftp://data.pdbj.org/pub/pdb/validation_reports/q2/7q28 | HTTPS FTP |
-Related structure data
Related structure data | 7q24C 7q25C 7q26C 7q27C 7q29C 6f9tS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 68861.875 Da / Num. of mol.: 1 / Mutation: E54G, N90Q, N155Q, N337Q, N586Q 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, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds, peptidyl-dipeptidase A |
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-Sugars , 2 types, 2 molecules
#2: Polysaccharide | alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-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 Source method: isolated from a genetically manipulated source |
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#3: Sugar | ChemComp-NAG / |
-Non-polymers , 7 types, 444 molecules
#4: Chemical | #5: Chemical | ChemComp-8J9 / ( | #6: Chemical | ChemComp-PEG / | #7: Chemical | #8: Chemical | ChemComp-ZN / | #9: Chemical | #10: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 46.81 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 4 / Details: 0.1 M MIB pH 4.0, 5% glycerol, 15% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 4, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→84.78 Å / Num. obs: 77571 / % possible obs: 100 % / Redundancy: 32.7 % / Biso Wilson estimate: 21.77 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.183 / Rpim(I) all: 0.032 / Net I/σ(I): 15.2 |
Reflection shell | Resolution: 1.65→1.68 Å / Redundancy: 22.1 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 3761 / CC1/2: 0.512 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6F9T Resolution: 1.65→71.55 Å / SU ML: 0.1694 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.3968 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.93 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.65→71.55 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A
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