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- PDB-5am9: Crystal structure of the Angiotensin-1 converting enzyme N-domain... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5am9 | |||||||||
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Title | Crystal structure of the Angiotensin-1 converting enzyme N-domain in complex with amyloid-beta 10-16 | |||||||||
![]() | ANGIOTENSIN-CONVERTING ENZYME | |||||||||
![]() | HYDROLASE / METALLOPROTEASE / AMYLOID- BETA | |||||||||
Function / homology | ![]() 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 / positive regulation of systemic arterial blood pressure / negative regulation of gap junction assembly / metallodipeptidase activity / cellular response to aldosterone / hormone catabolic process / bradykinin catabolic process / angiogenesis involved in coronary vascular morphogenesis / response to thyroid hormone / negative regulation of glucose import / vasoconstriction / neutrophil mediated immunity / regulation of smooth muscle cell migration / regulation of hematopoietic stem cell proliferation / antigen processing and presentation of peptide antigen via MHC class I / hormone metabolic process / 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 / arachidonate secretion / post-transcriptional regulation of gene expression / eating behavior / peptide catabolic process / lung alveolus development / heart contraction / heterocyclic compound binding / response to dexamethasone / regulation of heart rate by cardiac conduction / regulation of systemic arterial blood pressure by renin-angiotensin / regulation of vasoconstriction / hematopoietic stem cell differentiation / peptidyl-dipeptidase activity / blood vessel remodeling / amyloid-beta metabolic process / angiotensin maturation / 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 / male gonad development / metallopeptidase activity / peptidase activity / actin binding / spermatogenesis / endopeptidase activity / response to lipopolysaccharide / lysosome / response to hypoxia / calmodulin binding / endosome / response to xenobiotic stimulus / positive regulation of apoptotic process / external side of plasma membrane / negative regulation of gene expression / proteolysis / extracellular space / extracellular exosome / zinc ion binding / extracellular region / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Masuyer, G. / Larmuth, K.M. / Douglas, R.G. / Sturrock, E.D. / Acharya, K.R. | |||||||||
![]() | ![]() Title: The Kinetic and Structural Characterisation of Amyloid-Beta Metabolism by Human Angiotensin-1- Converting Enzyme (Ace) Authors: Larmuth, K.M. / Masuyer, G. / Douglas, R.G. / Sturrock, E.D. / Acharya, K.R. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1003 KB | Display | ![]() |
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PDB format | ![]() | 838.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5am8C ![]() 5amaC ![]() 5ambC ![]() 5amcC ![]() 3nxqS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 72606.508 Da / Num. of mol.: 4 / Fragment: N DOMAIN, UNP RESIDUES 30-658 / Mutation: YES Source method: isolated from a genetically manipulated source Details: MINIMALLY GLYCOSYLATED MUTANT / Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P12821, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds, peptidyl-dipeptidase A |
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-Sugars , 5 types, 12 molecules
#2: Polysaccharide | beta-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source | ||||||
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#3: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #4: Polysaccharide | Source method: isolated from a genetically manipulated source #5: Polysaccharide | Source method: isolated from a genetically manipulated source #6: Polysaccharide | Source method: isolated from a genetically manipulated source |
-Non-polymers , 11 types, 1687 molecules ![](data/chem/img/GLN.gif)
![](data/chem/img/LYS.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/P6G.gif)
![](data/chem/img/GLU.gif)
![](data/chem/img/VAL.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/LYS.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/P6G.gif)
![](data/chem/img/GLU.gif)
![](data/chem/img/VAL.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
#7: Chemical | #8: Chemical | #9: Chemical | ChemComp-ZN / #10: Chemical | ChemComp-CL / #11: Chemical | #12: Chemical | ChemComp-PEG / #13: Chemical | ChemComp-P6G / #14: Chemical | #15: Chemical | #16: Chemical | #17: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.95 Å3/Da / Density % sol: 58 % / Description: NONE |
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Crystal grow | pH: 8.5 Details: 0.06 M DIVALENT CATIONS, 0.1 M TRIS/BICINE PH 8.5, 30 % PEG550MME/PEG20000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 24, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→31.47 Å / Num. obs: 291734 / % possible obs: 97 % / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 5.3 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.76 / Mean I/σ(I) obs: 1.4 / % possible all: 95.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3NXQ Resolution: 1.8→113.27 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.945 / SU B: 8.626 / SU ML: 0.108 / Cross valid method: THROUGHOUT / ESU R: 0.125 / ESU R Free: 0.12 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. FOR AMYLOID-BETA FRAGMENT 10-16, ONLY DI-PEPTIDE PRODUCT OF THE ACE ENZYMATIC ACTIVITY WERE SEEN.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.347 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→113.27 Å
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Refine LS restraints |
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