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- PDB-5amb: 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: 5amb | |||||||||
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Title | Crystal structure of the Angiotensin-1 converting enzyme N-domain in complex with amyloid-beta 35-42 | |||||||||
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![]() | HYDROLASE / ANGIOTENSIN-CONVERTING ENZYME / 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 / 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 / regulation of epidermal growth factor-activated receptor activity / cytosolic mRNA polyadenylation / collateral sprouting in absence of injury / hormone metabolic process / neutrophil mediated immunity / microglia development / regulation of smooth muscle cell migration / regulation of hematopoietic stem cell proliferation / regulation of synapse structure or activity / regulation of Wnt signaling pathway / Formyl peptide receptors bind formyl peptides and many other ligands / axo-dendritic transport / synaptic assembly at neuromuscular junction / signaling receptor activator activity / smooth endoplasmic reticulum calcium ion homeostasis / axon midline choice point recognition / astrocyte activation involved in immune response / regulation of spontaneous synaptic transmission / mating behavior / NMDA selective glutamate receptor signaling pathway / mitogen-activated protein kinase binding / embryo development ending in birth or egg hatching / chloride ion binding / ciliary rootlet / mitogen-activated protein kinase kinase binding / positive regulation of neurogenesis / Lysosome Vesicle Biogenesis / PTB domain binding / Golgi-associated vesicle / arachidonic acid secretion / post-transcriptional regulation of gene expression / eating behavior / positive regulation of amyloid fibril formation / neuron remodeling / : / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / heterocyclic compound binding / lung alveolus development / heart contraction / peptide catabolic process / suckling behavior / nuclear envelope lumen / response to dexamethasone / dendrite development / COPII-coated ER to Golgi transport vesicle / presynaptic active zone / regulation of heart rate by cardiac conduction / modulation of excitatory postsynaptic potential / TRAF6 mediated NF-kB activation / Advanced glycosylation endproduct receptor signaling / regulation of systemic arterial blood pressure by renin-angiotensin / neuromuscular process controlling balance / The NLRP3 inflammasome / regulation of presynapse assembly / transition metal ion binding / negative regulation of long-term synaptic potentiation / regulation of multicellular organism growth / intracellular copper ion homeostasis / negative regulation of neuron differentiation / regulation of vasoconstriction / ECM proteoglycans / smooth endoplasmic reticulum / peptidyl-dipeptidase activity / hematopoietic stem cell differentiation / positive regulation of T cell migration / blood vessel remodeling / spindle midzone / angiotensin maturation / amyloid-beta metabolic process / animal organ regeneration / Metabolism of Angiotensinogen to Angiotensins / Purinergic signaling in leishmaniasis infection / positive regulation of calcium-mediated signaling / protein serine/threonine kinase binding / positive regulation of chemokine production / clathrin-coated pit 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 | ![]() | 556.3 KB | Display | ![]() |
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PDB format | ![]() | 457 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 2.8 MB | Display | ![]() |
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Full document | ![]() | 2.8 MB | Display | |
Data in XML | ![]() | 53.5 KB | Display | |
Data in CIF | ![]() | 79.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5am8C ![]() 5am9C ![]() 5amaC ![]() 5amcC ![]() 3nxqS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
-Protein / Protein/peptide , 2 types, 4 molecules ABPQ
#1: Protein | Mass: 72606.508 Da / Num. of mol.: 2 / Fragment: N DOMAIN, UNP RESIDUES 30-657 / Mutation: YES Source method: isolated from a genetically manipulated source Details: MINIMALLY GLYCOSYLATED MUTANT / Source: (gene. exp.) ![]() ![]() ![]() #2: Protein/peptide | Mass: 744.943 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 706-713 / Source method: obtained synthetically Details: ONLY DI-PEPTIDE ILE-ALA (41-42) VISIBLE IN STRUCTURE Source: (synth.) ![]() |
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-Sugars , 4 types, 6 molecules
#3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Polysaccharide | Source method: isolated from a genetically manipulated source #5: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...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 #6: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source |
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-Non-polymers , 6 types, 884 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/P6G.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/P6G.gif)
![](data/chem/img/HOH.gif)
#7: Chemical | #8: Chemical | #9: Chemical | ChemComp-PEG / #10: Chemical | ChemComp-PG4 / | #11: Chemical | #12: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.85 Å3/Da / Density % sol: 57 % / 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: Oct 13, 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: 1.5→29.6 Å / Num. obs: 209085 / % possible obs: 83.3 % / Observed criterion σ(I): 0 / Redundancy: 1.6 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 7.2 |
Reflection shell | Resolution: 1.5→1.58 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 1.1 / % possible all: 42.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3NXQ Resolution: 1.55→74.51 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.968 / SU B: 4.676 / SU ML: 0.068 / Cross valid method: THROUGHOUT / ESU R: 0.091 / ESU R Free: 0.072 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.55→74.51 Å
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Refine LS restraints |
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