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Yorodumi- PDB-2c6n: Structure of human somatic angiontensin-I converting enzyme N dom... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2c6n | ||||||||||||
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Title | Structure of human somatic angiontensin-I converting enzyme N domain with lisinopril | ||||||||||||
Components | ANGIOTENSIN-CONVERTING ENZYME, SOMATIC ISOFORM | ||||||||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / HYDROLASE / ANGIOTENSIN-I CONVERTING ENZYME / N DOMAIN / ZINC METALLOPEPTIDASE / METALLOPROTEASE / ANGIOTENSIN / LISINOPRIL / CARBOXYPEPTIDASE / GLYCOPROTEIN / METAL-BINDING / PHOSPHORYLATION / PROTEASE / TRANSMEMBRANE / HYDROLASE-HYDROLASE INHIBITOR COMPLEX | ||||||||||||
Function / homology | Function and homology information mononuclear cell proliferation / cell proliferation in bone marrow / bradykinin receptor binding / exopeptidase activity / regulation of angiotensin metabolic process / substance P catabolic process / peptidyl-dipeptidase A / positive regulation of systemic arterial blood pressure / tripeptidyl-peptidase activity / regulation of renal output by angiotensin ...mononuclear cell proliferation / cell proliferation in bone marrow / bradykinin receptor binding / exopeptidase activity / regulation of angiotensin metabolic process / substance P catabolic process / peptidyl-dipeptidase A / positive regulation of systemic arterial blood pressure / 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 / cellular response to aldosterone / hormone catabolic process / bradykinin catabolic process / angiogenesis involved in coronary vascular morphogenesis / response to thyroid hormone / negative regulation of D-glucose import / vasoconstriction / hormone metabolic process / 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 / 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 / heterocyclic compound binding / lung alveolus development / post-transcriptional regulation of gene expression / arachidonate secretion / eating behavior / peptide catabolic process / heart contraction / response to dexamethasone / regulation of heart rate by cardiac conduction / regulation of systemic arterial blood pressure by renin-angiotensin / blood vessel remodeling / hematopoietic stem cell differentiation / regulation of vasoconstriction / peptidyl-dipeptidase activity / animal organ regeneration / amyloid-beta metabolic process / angiotensin maturation / Metabolism of Angiotensinogen to Angiotensins / positive regulation of vasoconstriction / carboxypeptidase activity / sperm midpiece / blood vessel diameter maintenance / kidney development / basal plasma membrane / response to nutrient levels / 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 / positive regulation of apoptotic process / response to xenobiotic stimulus / 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: 3 Å | ||||||||||||
Authors | Corradi, H.R. / Schwager, S.L.U. / Nichinda, A. / Sturrock, E.D. / Acharya, K.R. | ||||||||||||
Citation | Journal: J. Mol. Biol. / Year: 2006 Title: Crystal structure of the N domain of human somatic angiotensin I-converting enzyme provides a structural basis for domain-specific inhibitor design. Authors: Corradi, H.R. / Schwager, S.L. / Nchinda, A.T. / 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 | 2c6n.cif.gz | 254.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2c6n.ent.gz | 200.8 KB | Display | PDB format |
PDBx/mmJSON format | 2c6n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2c6n_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 2c6n_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 2c6n_validation.xml.gz | 56 KB | Display | |
Data in CIF | 2c6n_validation.cif.gz | 74.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c6/2c6n ftp://data.pdbj.org/pub/pdb/validation_reports/c6/2c6n | HTTPS FTP |
-Related structure data
Related structure data | 2c6fC 1o8aS 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: 70536.148 Da / Num. of mol.: 2 / Fragment: N DOMAIN, RESIDUES 38-649 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: Q59GY8, UniProt: P12821*PLUS, peptidyl-dipeptidase A |
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-Sugars , 2 types, 6 molecules
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Sugar | ChemComp-NAG / |
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-Non-polymers , 6 types, 28 molecules
#4: Chemical | #5: Chemical | #6: Chemical | #7: Chemical | #8: Chemical | ChemComp-ACT / | #9: Water | ChemComp-HOH / | |
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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: 3.39 Å3/Da / Density % sol: 63.44 % |
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Crystal grow | pH: 4.9 Details: 0.2M LITHIUM SULPHATE, 0.1M SODIUM ACETATE, PH 4.9, 10UM ZINC SULPHATE, 18% POLYETHYLENE GLYCOL 4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 1.488 |
Detector | Type: ADSC CCD / Detector: CCD / Date: May 19, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.488 Å / Relative weight: 1 |
Reflection | Resolution: 3→50 Å / Num. obs: 36858 / % possible obs: 95.5 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Biso Wilson estimate: 50.2 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 10.2 |
Reflection shell | Resolution: 3→3.16 Å / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 2.2 / % possible all: 85.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1O8A Resolution: 3→28.76 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 2443102.53 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 39.17 Å2 / ksol: 0.35 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3→28.76 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.19 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 6
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Xplor file | Serial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: PROTEIN.TOP |