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- PDB-1utz: Crystal Structure of MMP-12 complexed to (2R)-3-({[4-[(pyridin-4-... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1utz | ||||||
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Title | Crystal Structure of MMP-12 complexed to (2R)-3-({[4-[(pyridin-4-yl)phenyl]-thien-2-yl}carboxamido)(phenyl)propanoic acid | ||||||
![]() | MACROPHAGE METALLOELASTASE | ||||||
![]() | HYDROLASE / MACROPHAGE METALLOELASTASE / NON-ZINC CHELATOR / MMP-12 / MMP INHIBITOR / METALLOPROTEASE | ||||||
Function / homology | ![]() 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 / negative regulation of type I interferon-mediated signaling pathway / lung alveolus development ...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 / negative regulation of type I interferon-mediated signaling pathway / lung alveolus development / response to amyloid-beta / positive regulation of interferon-alpha production / 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 | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | 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. | ||||||
![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 83.8 KB | Display | ![]() |
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PDB format | ![]() | 63.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1rosC ![]() 1uttC ![]() 1jk3S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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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 |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 17631.648 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN, RESIDUES 106-264 Source method: isolated from a genetically manipulated source Details: COMPLEXED WITH A SMALL MOLECULE INHIBITOR (2R)-3-({[4-[(PYRIDIN-4-YL)PHENYL]-THIEN-2-YL} CARBOXAMIDO)(PHENYL)PROPANOIC ACID FORMULA C25 H19 N2 O2 S AND ALSO WITH ACETOHYDROXAMIC ACID OR 2- ...Details: COMPLEXED WITH A SMALL MOLECULE INHIBITOR (2R)-3-({[4-[(PYRIDIN-4-YL)PHENYL]-THIEN-2-YL} CARBOXAMIDO)(PHENYL)PROPANOIC ACID FORMULA C25 H19 N2 O2 S AND ALSO WITH ACETOHYDROXAMIC ACID OR 2-HYDROXYAMINO -2-ETHANAL FORMULA, C2H5NO2 Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 144 molecules ![](data/chem/img/PF3.gif)
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#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-ZN / #5: Chemical | ChemComp-CA / #6: Water | ChemComp-HOH / | |
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-Details
Compound details | MAY BE INVOLVED IN TISSUE INJURY AND REMODELING |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.37 Å3/Da / Density % sol: 63.54 % |
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Crystal grow | Temperature: 293 K / pH: 8 / Details: 0.1M IMIDAZOLE PH 8.0, 2.0-2.5M NACL, 20 C |
-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ![]() |
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: 2.5→99 Å / Num. obs: 26781 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 6.98 % / Rmerge(I) obs: 0.143 / Net I/σ(I): 13.22 |
Reflection shell | Resolution: 2.5→2.56 Å / Redundancy: 6.46 % / Rmerge(I) obs: 0.446 / Mean I/σ(I) obs: 4.1 / % possible all: 99.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1JK3 Resolution: 2.5→30 Å / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 2.5→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.52 Å / Total num. of bins used: 50
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