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Yorodumi- PDB-2xyd: human Angiotenisn converting enzyme N-domain in complex with Phos... -
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-Basic information
Entry | Database: PDB / ID: 2xyd | |||||||||
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Title | human Angiotenisn converting enzyme N-domain in complex with Phosphinic tripeptide | |||||||||
Components | ANGIOTENSIN-CONVERTING ENZYME | |||||||||
Keywords | HYDROLASE / ZINC METALLOPEPTIDASE | |||||||||
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 / arachidonic acid secretion / post-transcriptional regulation of gene expression / eating behavior / 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: 2.15 Å | |||||||||
Authors | Akif, M. / Schwager, S.L. / Anthony, C.S. / Czarny, B. / Beau, F. / Dive, V. / Sturrock, E.D. / Acharya, K.R. | |||||||||
Citation | Journal: Biochem.J. / Year: 2011 Title: Novel Mechanism of Inhibition of Human Angiotensin-I-Converting Enzyme (Ace) by a Highly Specific Phosphinic Tripeptide. Authors: Akif, M. / Schwager, S.L. / Anthony, C.S. / Czarny, B. / Beau, F. / Dive, V. / 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 | 2xyd.cif.gz | 266.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xyd.ent.gz | 212.7 KB | Display | PDB format |
PDBx/mmJSON format | 2xyd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xy/2xyd ftp://data.pdbj.org/pub/pdb/validation_reports/xy/2xyd | HTTPS FTP |
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-Related structure data
Related structure data | 2xy9C 3nxqS C: citing same article (ref.) 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: 70423.148 Da / Num. of mol.: 2 / Fragment: RESIDUES 30-639 / Mutation: YES Source method: isolated from a genetically manipulated source Details: FINAL CONSTRUCT IS UNDERGLYCOSYALTED MUTANT AND CONTAINS TWO MISMATCH MUTATIONS, P576L AND Q545R Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PCDNA3.1 / Cell line (production host): CHO K1 / Production host: CRICETULUS GRISEUS (Chinese hamster) / References: UniProt: P12821, peptidyl-dipeptidase A |
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-Sugars , 4 types, 6 molecules
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #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 |
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-Non-polymers , 7 types, 254 molecules
#6: Chemical | #7: Chemical | #8: Chemical | #9: Chemical | ChemComp-PEG / #10: Chemical | #11: Chemical | ChemComp-P6G / | #12: Water | ChemComp-HOH / | |
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-Details
Compound details | ENGINEERED RESIDUE IN CHAIN A, ASN 38 TO GLN ENGINEERED RESIDUE IN CHAIN A, ASN 54 TO GLN ...ENGINEERED |
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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: 2.87 Å3/Da / Density % sol: 57.1 % / 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 / Wavelength: 0.9763 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Oct 23, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→50 Å / Num. obs: 84896 / % possible obs: 97 % / Observed criterion σ(I): 2 / Redundancy: 2.5 % / Biso Wilson estimate: 34.57 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 14.1 |
Reflection shell | Resolution: 2.15→2.19 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 2.4 / % possible all: 95 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3NXQ Resolution: 2.15→40.28 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.917 / SU B: 5.912 / SU ML: 0.155 / Cross valid method: THROUGHOUT / ESU R: 0.258 / ESU R Free: 0.205 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES A130-A132 ARE DISORDERED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.877 Å2
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Refinement step | Cycle: LAST / Resolution: 2.15→40.28 Å
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Refine LS restraints |
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