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Yorodumi- PDB-2ddy: Solution Structure of Matrilysin (MMP-7) Complexed to Constraint ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ddy | ||||||
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Title | Solution Structure of Matrilysin (MMP-7) Complexed to Constraint Conformational Sulfonamide Inhibitor | ||||||
Components | Matrilysin | ||||||
Keywords | HYDROLASE / matrix metalloproteinase / matrilysin / complex / MMP-7 / solution structure / madw01053 | ||||||
Function / homology | Function and homology information matrilysin / antibacterial peptide secretion / antibacterial peptide biosynthetic process / membrane protein intracellular domain proteolysis / Assembly of collagen fibrils and other multimeric structures / Activation of Matrix Metalloproteinases / Collagen degradation / membrane protein ectodomain proteolysis / collagen catabolic process / extracellular matrix disassembly ...matrilysin / antibacterial peptide secretion / antibacterial peptide biosynthetic process / membrane protein intracellular domain proteolysis / Assembly of collagen fibrils and other multimeric structures / Activation of Matrix Metalloproteinases / Collagen degradation / membrane protein ectodomain proteolysis / collagen catabolic process / extracellular matrix disassembly / Degradation of the extracellular matrix / extracellular matrix / extracellular matrix organization / metalloendopeptidase activity / metallopeptidase activity / regulation of cell population proliferation / endopeptidase activity / defense response to Gram-negative bacterium / Extra-nuclear estrogen signaling / positive regulation of cell migration / defense response to Gram-positive bacterium / response to xenobiotic stimulus / serine-type endopeptidase activity / proteolysis / extracellular space / zinc ion binding / extracellular exosome / extracellular region Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / distance geometry simulated annealing torsion angle dynamics | ||||||
Authors | Zheng, X.H. / Ou, L. | ||||||
Citation | Journal: to be published Title: Solution Structure of Matrilysin (MMP-7) Complexed to Constraint Conformational Sulfonamide Inhibitor Authors: Zheng, X.H. / Ou, L. / Zhang, Q. / Wu, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ddy.cif.gz | 1.4 MB | Display | PDBx/mmCIF format |
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PDB format | pdb2ddy.ent.gz | 1.1 MB | Display | PDB format |
PDBx/mmJSON format | 2ddy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ddy_validation.pdf.gz | 457.9 KB | Display | wwPDB validaton report |
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Full document | 2ddy_full_validation.pdf.gz | 608.6 KB | Display | |
Data in XML | 2ddy_validation.xml.gz | 96.3 KB | Display | |
Data in CIF | 2ddy_validation.cif.gz | 116.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dd/2ddy ftp://data.pdbj.org/pub/pdb/validation_reports/dd/2ddy | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 19157.465 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET11C / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P09237, matrilysin | ||||
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#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-MDW / ( | |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||
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NMR experiment |
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NMR details | Text: The structure was determined using triple-resonance NMR spectroscopy |
-Sample preparation
Details | Contents: 0.7mM MMP7 U-15N, 13C; 10mM deuterated Tris, 10mM CaCl2, 0.1mM ZnCl2, 0.1M NaCl; 90% H2O, 10% D2O Solvent system: 90% H2O/10% D2O |
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Sample conditions | Ionic strength: 0.1M NaCl / pH: 6.8 / Pressure: ambient / Temperature: 310 K |
-NMR measurement
NMR spectrometer | Type: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz |
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-Processing
NMR software |
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Refinement | Method: distance geometry simulated annealing torsion angle dynamics Software ordinal: 1 | ||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: target function / Conformers calculated total number: 200 / Conformers submitted total number: 25 |