[English] 日本語
Yorodumi- PDB-1utt: Crystal Structure of MMP-12 complexed to 2-(1,3-dioxo-1,3-dihydro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1utt | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of MMP-12 complexed to 2-(1,3-dioxo-1,3-dihydro-2H-isoindol-2-yl)ethyl-4-(4-ethoxy[1,1-biphenyl]-4-yl)-4-oxobutanoic acid | ||||||
Components | MACROPHAGE METALLOELASTASE | ||||||
Keywords | HYDROLASE / MACROPHAGE METALLOELASTASE / NON-ZINC CHELATOR / MMP-12 / MMP INHIBITOR / METALLOPROTEASE | ||||||
Function / homology | Function and homology information macrophage elastase / negative regulation of endothelial cell-matrix adhesion via fibronectin / bronchiole development / positive regulation of epithelial cell proliferation involved in wound healing / elastin catabolic process / regulation of defense response to virus by host / positive regulation of type I interferon-mediated signaling pathway / wound healing, spreading of epidermal cells / lung alveolus development / negative regulation of type I interferon-mediated signaling pathway ...macrophage elastase / negative regulation of endothelial cell-matrix adhesion via fibronectin / bronchiole development / positive regulation of epithelial cell proliferation involved in wound healing / elastin catabolic process / regulation of defense response to virus by host / positive regulation of type I interferon-mediated signaling pathway / wound healing, spreading of epidermal cells / lung alveolus development / negative regulation of type I interferon-mediated signaling pathway / positive regulation of interferon-alpha production / response to amyloid-beta / Collagen degradation / collagen catabolic process / extracellular matrix disassembly / core promoter sequence-specific DNA binding / collagen binding / Degradation of the extracellular matrix / extracellular matrix / extracellular matrix organization / cellular response to virus / metalloendopeptidase activity / protein import into nucleus / endopeptidase activity / sequence-specific DNA binding / serine-type endopeptidase activity / calcium ion binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / proteolysis / extracellular space / zinc ion binding / extracellular region / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Morales, R. / Perrier, S. / Florent, J.M. / Beltra, J. / Dufour, S. / De Mendez, I. / Manceau, P. / Tertre, A. / Moreau, F. / Compere, D. ...Morales, R. / Perrier, S. / Florent, J.M. / Beltra, J. / Dufour, S. / De Mendez, I. / Manceau, P. / Tertre, A. / Moreau, F. / Compere, D. / Dublanchet, A.C. / O'Gara, M. | ||||||
Citation | Journal: J. Mol. Biol. / Year: 2004 Title: Crystal structures of novel non-peptidic, non-zinc chelating inhibitors bound to MMP-12. Authors: Morales, R. / Perrier, S. / Florent, J.M. / Beltra, J. / Dufour, S. / De Mendez, I. / Manceau, P. / Tertre, A. / Moreau, F. / Compere, D. / Dublanchet, A.C. / O'Gara, M. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1utt.cif.gz | 51.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1utt.ent.gz | 35.4 KB | Display | PDB format |
PDBx/mmJSON format | 1utt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1utt_validation.pdf.gz | 722.3 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1utt_full_validation.pdf.gz | 724.4 KB | Display | |
Data in XML | 1utt_validation.xml.gz | 10 KB | Display | |
Data in CIF | 1utt_validation.cif.gz | 13.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ut/1utt ftp://data.pdbj.org/pub/pdb/validation_reports/ut/1utt | HTTPS FTP |
-Related structure data
Related structure data | 1rosC 1utzC 1jk3S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| x 6||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
| ||||||||
Details | OUR DYNAMIC LIGHT SCATTERING EXPERIMENTS HAVE SHOWN THATTHE PROTEIN EXISTS AS A MONOMER IN SOLUTION, SUGGESTINGTHAT THE HEXAMER DESCRIBED IN REMARK 350 IS AN ARTIFACTOF CRYSTALLIZATION ONLY. THE PROTEIN IS KNOWN TO FUNCTIONAS A MONOMER |
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 17631.648 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, RESIDUES 106-264 Source method: isolated from a genetically manipulated source Details: COMPLEXED WITH A SMALL MOLECULE INHIBITOR 2-(1,3-DIOXO-1,3-DIHYDRO-2H-ISOINDOL-2-YL)ETHYL-4-(4-ETHOXY[1,1-BIPHENYL]-4-YL)-4-OXOBUTANOIC ACID FORMULA C19H19N2O4S, AND ALSO WITH ...Details: COMPLEXED WITH A SMALL MOLECULE INHIBITOR 2-(1,3-DIOXO-1,3-DIHYDRO-2H-ISOINDOL-2-YL)ETHYL-4-(4-ETHOXY[1,1-BIPHENYL]-4-YL)-4-OXOBUTANOIC ACID FORMULA C19H19N2O4S, AND ALSO WITH ACETOHYDROXAMIC ACID OR 2-HYDROXYAMINO-2-ETHANAL FORMULA, C2H5NO2 Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGEMEX1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P39900, macrophage elastase |
---|
-Non-polymers , 5 types, 105 molecules
#2: Chemical | ChemComp-HAE / | ||||
---|---|---|---|---|---|
#3: Chemical | ChemComp-CP8 / | ||||
#4: Chemical | #5: Chemical | ChemComp-CA / #6: Water | ChemComp-HOH / | |
-Details
Compound details | MAY BE INVOLVED IN TISSUE INJURY AND REMODELING. HAS SIGNIFICANT ELASTOLYTIC ACTIVITY. BINDS 2 ZINC ...MAY BE INVOLVED IN TISSUE INJURY AND REMODELING |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 4.2 Å3/Da / Density % sol: 71 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1M SODIUM CACODYLATE PH 6.4, 1.4M AMMONIUM ACETATE, 4 C |
-Data collection
Diffraction | Mean temperature: 293 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 |
Detector | Type: RIGAKU-MSC RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 15, 2002 / Details: RIGAKU-MSC OSMIC MIRRORS |
Radiation | Monochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→30 Å / Num. obs: 17420 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 6.98 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 25.63 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 24 % / Rmerge(I) obs: 0.406 / Mean I/σ(I) obs: 4.74 / % possible all: 99.8 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1JK3 Resolution: 2.2→30 Å / σ(F): 0
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→30 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2→2.25 Å / Total num. of bins used: 16
|