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- PDB-4h1q: Crystal structure of mutant MMP-9 catalytic domain in complex wit... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4h1q | ||||||
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Title | Crystal structure of mutant MMP-9 catalytic domain in complex with a twin inhibitor. | ||||||
![]() | Matrix metalloproteinase-9 | ||||||
![]() | HYDROLASE/HYDROLASE inhibitor / HYDROLASE/TWIN INHIBITOR / Zincin-like / Gelatinase / Collagenase (Catalytic Domain) / HYDROLASE-HYDROLASE inhibitor complex | ||||||
Function / homology | ![]() gelatinase B / negative regulation of epithelial cell differentiation involved in kidney development / negative regulation of cation channel activity / negative regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway / cellular response to UV-A / positive regulation of keratinocyte migration / regulation of neuroinflammatory response / positive regulation of epidermal growth factor receptor signaling pathway / Assembly of collagen fibrils and other multimeric structures / Activation of Matrix Metalloproteinases ...gelatinase B / negative regulation of epithelial cell differentiation involved in kidney development / negative regulation of cation channel activity / negative regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway / cellular response to UV-A / positive regulation of keratinocyte migration / regulation of neuroinflammatory response / positive regulation of epidermal growth factor receptor signaling pathway / Assembly of collagen fibrils and other multimeric structures / Activation of Matrix Metalloproteinases / endodermal cell differentiation / positive regulation of release of cytochrome c from mitochondria / response to amyloid-beta / macrophage differentiation / Collagen degradation / collagen catabolic process / EPH-ephrin mediated repulsion of cells / extracellular matrix disassembly / ephrin receptor signaling pathway / positive regulation of DNA binding / negative regulation of intrinsic apoptotic signaling pathway / positive regulation of vascular associated smooth muscle cell proliferation / collagen binding / cellular response to cadmium ion / embryo implantation / Degradation of the extracellular matrix / extracellular matrix organization / positive regulation of receptor binding / skeletal system development / Signaling by SCF-KIT / metalloendopeptidase activity / cellular response to reactive oxygen species / metallopeptidase activity / cell migration / tertiary granule lumen / peptidase activity / cellular response to lipopolysaccharide / Interleukin-4 and Interleukin-13 signaling / collagen-containing extracellular matrix / endopeptidase activity / ficolin-1-rich granule lumen / Extra-nuclear estrogen signaling / positive regulation of protein phosphorylation / positive regulation of apoptotic process / serine-type endopeptidase activity / apoptotic process / Neutrophil degranulation / negative regulation of apoptotic process / proteolysis / extracellular space / zinc ion binding / extracellular exosome / extracellular region / identical protein binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Stura, E.A. / Vera, L. / Cassar-Lajeunesse, E. / Nuti, E. / Catalani, M.P. / Dive, V. / Rossello, A. | ||||||
![]() | ![]() Title: Crystallization of bi-functional ligand protein complexes. Authors: Antoni, C. / Vera, L. / Devel, L. / Catalani, M.P. / Czarny, B. / Cassar-Lajeunesse, E. / Nuti, E. / Rossello, A. / Dive, V. / Stura, E.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 95.4 KB | Display | ![]() |
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PDB format | ![]() | 71.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1013.9 KB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 21.9 KB | Display | |
Data in CIF | ![]() | 29.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4h2eC ![]() 4h30C ![]() 4h3xC ![]() 4h49C ![]() 4h76C ![]() 4h82C ![]() 4h84C ![]() 4hmaC ![]() 4i03C ![]() 2ow1S 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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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 17932.871 Da / Num. of mol.: 2 / Fragment: unp residues 110-214 / Mutation: E402Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-CA / #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.99 Å3/Da / Density % sol: 38.04 % |
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Crystal grow | Temperature: 293 K / pH: 8 Details: Protein: MMP9h Nter=GFQT E402Q V391Q at 130.3 micro-M with 5 milli-M AHA Reservoir: 40% MPEG 5K, 100mM HEPES. Cryoprotectant: 35% MPEG 5K, 15% PEG 400, 15% AAB (90/10), pH 8.0, VAPOR ...Details: Protein: MMP9h Nter=GFQT E402Q V391Q at 130.3 micro-M with 5 milli-M AHA Reservoir: 40% MPEG 5K, 100mM HEPES. Cryoprotectant: 35% MPEG 5K, 15% PEG 400, 15% AAB (90/10), pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4r / Detector: CCD / Date: Nov 24, 2010 / Details: MIRRORS |
Radiation | Monochromator: DIAMOND (111), GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9334 Å / Relative weight: 1 |
Reflection | Resolution: 1.59→50 Å / Num. obs: 36921 / % possible obs: 96.8 % / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Biso Wilson estimate: 21.71 Å2 / Rmerge(I) obs: 0.0124 / Rsym value: 0.109 / Net I/σ(I): 11.53 |
Reflection shell | Resolution: 1.59→1.68 Å / Redundancy: 4.06 % / Rmerge(I) obs: 1.229 / Mean I/σ(I) obs: 1.35 / Rsym value: 1.076 / % possible all: 94.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2OW1 Resolution: 1.59→43.09 Å / SU ML: 0.19 / Isotropic thermal model: Isotropic / σ(F): 1.99 / Phase error: 20.91 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.59→43.09 Å
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Refine LS restraints |
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LS refinement shell |
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