[English] 日本語
![](img/lk-miru.gif)
- PDB-4xct: Crystal structure of a hydroxamate based inhibitor ARP101 (EN73) ... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 4xct | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of a hydroxamate based inhibitor ARP101 (EN73) in complex with the MMP-9 catalytic domain. | |||||||||
![]() | Matrix metalloproteinase-9,Matrix metalloproteinase-9 | |||||||||
![]() | HYDROLASE / Inhibitor-complex / metalloprotease | |||||||||
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 / 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 / EPH-ephrin mediated repulsion of cells / extracellular matrix disassembly / ephrin receptor signaling pathway / 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 / Neutrophil degranulation / apoptotic process / 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. / Tepshi, L. / Nuti, E. / Dive, V. / Cassar-Lajeunesse, E. / Vera, L. / Rossello, A. | |||||||||
![]() | ![]() Title: N-O-Isopropyl Sulfonamido-Based Hydroxamates as Matrix Metalloproteinase Inhibitors: Hit Selection and in Vivo Antiangiogenic Activity. Authors: Nuti, E. / Cantelmo, A.R. / Gallo, C. / Bruno, A. / Bassani, B. / Camodeca, C. / Tuccinardi, T. / Vera, L. / Orlandini, E. / Nencetti, S. / Stura, E.A. / Martinelli, A. / Dive, V. / Albini, A. / Rossello, A. | |||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 102.6 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 76.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 4wzvC ![]() 4h3xS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
| ||||||||||||
Components on special symmetry positions |
|
-
Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 17571.518 Da / Num. of mol.: 1 / Fragment: UNP residues 113-216,UNP residues 392-444 Source method: isolated from a genetically manipulated source Details: N73 zinc chelating inhibitor - human wild-type MMP-9 catalytic domain unp residues 107-215/391-443 Source: (gene. exp.) ![]() ![]() ![]() |
---|
-Non-polymers , 9 types, 246 molecules ![](data/chem/img/N73.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/PGO.gif)
![](data/chem/img/BUD.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/PGO.gif)
![](data/chem/img/BUD.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-N73 / ( | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
#3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-EDO / #7: Chemical | ChemComp-GOL / | #8: Chemical | #9: Chemical | ChemComp-BUD / ( | #10: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.07 Å3/Da / Density % sol: 40.47 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: protein: hMMP-9-WT at 337 micro-M with 120 milli-M acetohydroxamic acid. precipitant: 40.5% MPEG 5,000, 180 mM imidazole piperidine, pH 8.5. Cryoprotectant: 40% CryoProtX-C1, 10% PEG 10K, 10% PCTP 50/50 PH range: 7.0-8.5 / Temp details: constant incubator |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 16, 2014 / Details: mirrors |
Radiation | Monochromator: Channel cut Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97857 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→52 Å / Num. all: 38096 / Num. obs: 38007 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.2 % / Rmerge(I) obs: 0.06 / Rsym value: 0.055 / Net I/σ(I): 14.62 |
Reflection shell | Resolution: 1.3→1.38 Å / Redundancy: 6.16 % / Rmerge(I) obs: 1.392 / Mean I/σ(I) obs: 1.12 / % possible all: 99.1 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 4H3X Resolution: 1.3→34.295 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 32.17 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.3→34.295 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|