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Yorodumi- PDB-4bxk: Crystal structure of the Angiotensin-1 converting enzyme N-domain... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4bxk | |||||||||
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Title | Crystal structure of the Angiotensin-1 converting enzyme N-domain in complex with a domain-specific inhibitor | |||||||||
Components | ANGIOTENSIN-CONVERTING ENZYME | |||||||||
Keywords | HYDROLASE / METALLOPROTEASE / PROTEASE INHIBITOR | |||||||||
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 / eating behavior / post-transcriptional regulation of gene expression / 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 / hematopoietic stem cell differentiation / peptidyl-dipeptidase activity / blood vessel remodeling / amyloid-beta metabolic process / angiotensin maturation / animal organ regeneration / Metabolism of Angiotensinogen to Angiotensins / positive regulation of vasoconstriction / carboxypeptidase activity / 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 / peptidase activity / actin binding / 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: 2.2 Å | |||||||||
Authors | Douglas, R.G. / Sharma, R.K. / Masuyer, G. / Lubbe, L. / Zamora, I. / Acharya, K.R. / Chibale, K. / Sturrock, E.D. | |||||||||
Citation | Journal: Clin.Sci. / Year: 2014 Title: Fragment-Based Design for the Development of N-Domain Selective Angiotensin-1 Converting Enzyme Inhibitors Authors: Douglas, R.G. / Sharma, R.K. / Masuyer, G. / Lubbe, L. / Zamora, I. / Acharya, K.R. / Chibale, K. / 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 | 4bxk.cif.gz | 509.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4bxk.ent.gz | 417.1 KB | Display | PDB format |
PDBx/mmJSON format | 4bxk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4bxk_validation.pdf.gz | 2.9 MB | Display | wwPDB validaton report |
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Full document | 4bxk_full_validation.pdf.gz | 2.9 MB | Display | |
Data in XML | 4bxk_validation.xml.gz | 48.2 KB | Display | |
Data in CIF | 4bxk_validation.cif.gz | 68.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bx/4bxk ftp://data.pdbj.org/pub/pdb/validation_reports/bx/4bxk | HTTPS FTP |
-Related structure data
Related structure data | 3nxqS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 72606.508 Da / Num. of mol.: 2 / Fragment: N DOMAIN, RESIDUES 30-657 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): CHO-K1 / 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 , 5 types, 6 molecules
#2: Polysaccharide | 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: Polysaccharide | Source method: isolated from a genetically manipulated source #4: 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 #5: 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 #12: Sugar | ChemComp-NAG / | |
-Non-polymers , 7 types, 423 molecules
#6: Chemical | ChemComp-PEG / #7: Chemical | #8: Chemical | #9: Chemical | #10: Chemical | #11: Chemical | ChemComp-PG4 / | #13: Water | ChemComp-HOH / | |
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-Details
Sequence details | N-DOMAIN WITH MUTATIONS N9Q, N25Q, N82Q, N117Q, N131Q, N289Q, Q545R, P576L, R629L (SIMILAR ...N-DOMAIN WITH MUTATIONS N9Q, N25Q, N82Q, N117Q, N131Q, N289Q, Q545R, P576L, R629L (SIMILAR CONSTRUCT TO PDB 3NXQ) |
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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: 2.95 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: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 3, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→29.67 Å / Num. obs: 73018 / % possible obs: 91.4 % / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 10.5 |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.85 / Mean I/σ(I) obs: 2.6 / % possible all: 88.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3NXQ Resolution: 2.2→29.69 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.932 / SU B: 11.844 / SU ML: 0.146 / Cross valid method: THROUGHOUT / ESU R: 0.272 / ESU R Free: 0.199 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 130-132 ARE DISORDERED
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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: 28.232 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→29.69 Å
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Refine LS restraints |
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