+Open data
-Basic information
Entry | Database: PDB / ID: 2ovx | ||||||
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Title | MMP-9 active site mutant with barbiturate inhibitor | ||||||
Components | Matrix metalloproteinase-9 (EC 3.4.24.35) (MMP-9) (92 kDa type IV collagenase) (92 kDa gelatinase) (Gelatinase B) (GELB) | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / MATRIX METALLOPROTEINASE / S1-PRIME POCKET / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | Function and homology information 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 / positive regulation of DNA binding ...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 / positive regulation of DNA binding / 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 / cellular response to cadmium ion / extracellular matrix disassembly / EPH-ephrin mediated repulsion of cells / ephrin receptor signaling pathway / negative regulation of intrinsic apoptotic signaling pathway / positive regulation of vascular associated smooth muscle cell proliferation / collagen binding / embryo implantation / Degradation of the extracellular matrix / extracellular matrix organization / positive regulation of receptor binding / skeletal system development / cellular response to reactive oxygen species / Signaling by SCF-KIT / metalloendopeptidase activity / metallopeptidase activity / cell migration / tertiary granule lumen / peptidase activity / endopeptidase activity / cellular response to lipopolysaccharide / Interleukin-4 and Interleukin-13 signaling / collagen-containing extracellular matrix / Extra-nuclear estrogen signaling / ficolin-1-rich granule lumen / positive regulation of protein phosphorylation / positive regulation of apoptotic process / serine-type endopeptidase activity / Neutrophil degranulation / negative regulation of apoptotic process / apoptotic process / proteolysis / extracellular space / zinc ion binding / extracellular exosome / extracellular region / identical protein binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Tochowicz, A. / Bode, W. / Maskos, K. / Goettig, P. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2007 Title: Crystal Structures of MMP-9 Complexes with Five Inhibitors: Contribution of the Flexible Arg424 Side-chain to Selectivity. Authors: Tochowicz, A. / Maskos, K. / Huber, R. / Oltenfreiter, R. / Dive, V. / Yiotakis, A. / Zanda, M. / Bode, W. / Goettig, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ovx.cif.gz | 87.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ovx.ent.gz | 64.8 KB | Display | PDB format |
PDBx/mmJSON format | 2ovx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ovx_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 2ovx_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 2ovx_validation.xml.gz | 17.2 KB | Display | |
Data in CIF | 2ovx_validation.cif.gz | 23.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ov/2ovx ftp://data.pdbj.org/pub/pdb/validation_reports/ov/2ovx | HTTPS FTP |
-Related structure data
Related structure data | 2ovzC 2ow0C 2ow1C 2ow2C 1gkdS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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3 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 17875.818 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN RESIDUES: 110-215, 391-443 / Mutation: E402Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MMP9, CLG4B / Production host: Escherichia coli (E. coli) / References: UniProt: P14780, gelatinase B |
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-Non-polymers , 5 types, 212 molecules
#2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-CA / #4: Chemical | ChemComp-CL / #5: Chemical | #6: 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: 2.76 Å3/Da / Density % sol: 55.48 % |
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Crystal grow | Temperature: 293 K / pH: 5 Details: 3.0 M NaCl, 0.1 M citric acid, VAPOR DIFFUSION, SITTING DROP, temperature 293K, pH 5.00 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.05 |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Jun 28, 2004 / Details: MIRRORS |
Radiation | Monochromator: SI 111 DOUBLE CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.05 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→99 Å / Num. obs: 29659 / % possible obs: 96.7 % / Observed criterion σ(I): 1 / Biso Wilson estimate: 16.2 Å2 / Rmerge(I) obs: 0.103 / Net I/σ(I): 13.2 |
Reflection shell | Resolution: 1.95→1.98 Å / Rmerge(I) obs: 0.395 / Mean I/σ(I) obs: 2.1 / % possible all: 95.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1GKD Resolution: 2→19.64 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 2233671.92 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 53.07 Å2 / ksol: 0.39 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→19.64 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
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Xplor file |
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