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Yorodumi- PDB-6f9u: Crystal structure of human testis Angiotensin-1 converting enzyme... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6f9u | |||||||||
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Title | Crystal structure of human testis Angiotensin-1 converting enzyme in complex with Sampatrilat-Asp. | |||||||||
Components | Angiotensin-converting enzyme | |||||||||
Keywords | HYDROLASE / Angiotensin-1 converting enzyme / ACE inhibitor / Sampatrilat / Sampatrilat-Asp | |||||||||
Function / homology | Function and homology information mononuclear cell proliferation / cell proliferation in bone marrow / tripeptidyl-peptidase activity / bradykinin receptor binding / regulation of angiotensin metabolic process / exopeptidase activity / substance P catabolic process / response to laminar fluid shear stress / peptidyl-dipeptidase A / regulation of renal output by angiotensin ...mononuclear cell proliferation / cell proliferation in bone marrow / tripeptidyl-peptidase activity / bradykinin receptor binding / regulation of angiotensin metabolic process / exopeptidase activity / substance P catabolic process / response to laminar fluid shear stress / peptidyl-dipeptidase A / regulation of renal output by angiotensin / negative regulation of calcium ion import / positive regulation of peptidyl-cysteine S-nitrosylation / 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 / hormone metabolic process / regulation of hematopoietic stem cell proliferation / regulation of smooth muscle cell migration / antigen processing and presentation of peptide antigen via MHC class I / mitogen-activated protein kinase binding / embryo development ending in birth or egg hatching / positive regulation of neurogenesis / chloride ion binding / mitogen-activated protein kinase kinase binding / eating behavior / arachidonic acid secretion / post-transcriptional regulation of gene expression / lung alveolus development / peptide catabolic process / heterocyclic compound binding / heart contraction / 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 / angiotensin maturation / hematopoietic stem cell differentiation / blood vessel remodeling / Metabolism of Angiotensinogen to Angiotensins / animal organ regeneration / amyloid-beta metabolic process / carboxypeptidase activity / positive regulation of vasoconstriction / sperm midpiece / blood vessel diameter maintenance / response to nutrient levels / basal plasma membrane / kidney development / female pregnancy / angiotensin-activated signaling pathway / cellular response to glucose stimulus / brush border membrane / regulation of synaptic plasticity / metalloendopeptidase activity / regulation of blood pressure / male gonad development / metallopeptidase activity / actin binding / peptidase activity / 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 | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | |||||||||
Authors | Cozier, G.E. / Acharya, K.R. | |||||||||
Funding support | United Kingdom, 1items
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Citation | Journal: FEBS J. / Year: 2018 Title: Crystal structures of sampatrilat and sampatrilat-Asp in complex with human ACE - a molecular basis for domain selectivity. Authors: Cozier, G.E. / Schwager, S.L. / Sharma, R.K. / Chibale, K. / Sturrock, E.D. / Acharya, K.R. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6f9u.cif.gz | 254.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6f9u.ent.gz | 202.4 KB | Display | PDB format |
PDBx/mmJSON format | 6f9u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f9/6f9u ftp://data.pdbj.org/pub/pdb/validation_reports/f9/6f9u | HTTPS FTP |
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-Related structure data
Related structure data | 6f9rC 6f9tC 6f9vC 1o8aS 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: 68281.234 Da / Num. of mol.: 1 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-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-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 , 9 types, 356 molecules
#4: Chemical | ChemComp-ZN / | ||||||||||||||
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#5: Chemical | #6: Chemical | ChemComp-1PE / | #7: Chemical | ChemComp-D0W / | #8: Chemical | ChemComp-BO3 / | #9: Chemical | #10: Chemical | ChemComp-EDO / #11: Chemical | ChemComp-PEG / | #12: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.85 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 4 / Details: 0.1 M MIB Buffer pH 4.0, 5% Glycerol, 15% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 20, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→85.86 Å / Num. obs: 51795 / % possible obs: 100 % / Redundancy: 25 % / CC1/2: 0.997 / Net I/σ(I): 9.3 |
Reflection shell | Resolution: 1.9→1.94 Å / Redundancy: 21.7 % / Mean I/σ(I) obs: 1.3 / Num. unique obs: 3303 / CC1/2: 0.576 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1O8A Resolution: 1.9→72.173 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.63
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→72.173 Å
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Refine LS restraints |
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LS refinement shell |
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