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- PDB-3nzi: Substrate induced remodeling of the active site regulates HtrA1 a... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3nzi | ||||||
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Title | Substrate induced remodeling of the active site regulates HtrA1 activity | ||||||
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![]() | hydrolase/hydrolase substrate / serine protease / DegP / HtrA / protease / hydrolase-peptide inhibitor complex / hydrolase-hydrolase substrate complex | ||||||
Function / homology | ![]() acyltransferase activity, acyl groups converted into alkyl on transfer / Citric acid cycle (TCA cycle) / citrate (Si)-synthase / chorionic trophoblast cell differentiation / citrate (Si)-synthase activity / acetyl-CoA metabolic process / citrate metabolic process / oxaloacetate metabolic process / programmed cell death / growth factor binding ...acyltransferase activity, acyl groups converted into alkyl on transfer / Citric acid cycle (TCA cycle) / citrate (Si)-synthase / chorionic trophoblast cell differentiation / citrate (Si)-synthase activity / acetyl-CoA metabolic process / citrate metabolic process / oxaloacetate metabolic process / programmed cell death / growth factor binding / negative regulation of BMP signaling pathway / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / tricarboxylic acid cycle / Degradation of the extracellular matrix / serine-type peptidase activity / molecular function activator activity / negative regulation of transforming growth factor beta receptor signaling pathway / placenta development / collagen-containing extracellular matrix / carbohydrate metabolic process / mitochondrial matrix / positive regulation of apoptotic process / serine-type endopeptidase activity / mitochondrion / proteolysis / extracellular space / extracellular exosome / extracellular region / identical protein binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Truebestein, L. / Tennstaedt, A. / Hauske, P. / Krojer, T. / Kaiser, M. / Clausen, T. / Ehrmann, M. | ||||||
![]() | ![]() Title: Substrate-induced remodeling of the active site regulates human HTRA1 activity. Authors: Truebestein, L. / Tennstaedt, A. / Monig, T. / Krojer, T. / Canellas, F. / Kaiser, M. / Clausen, T. / Ehrmann, 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 | ![]() | 57.8 KB | Display | ![]() |
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PDB format | ![]() | 39.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 433.5 KB | Display | ![]() |
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Full document | ![]() | 437 KB | Display | |
Data in XML | ![]() | 10.4 KB | Display | |
Data in CIF | ![]() | 12.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3numC ![]() 3nwuC ![]() 1lcyS C: citing same article ( S: Starting model for refinement |
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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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Components
#1: Protein | Mass: 36685.902 Da / Num. of mol.: 1 / Fragment: unp residues 158-480 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q92743, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases |
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#2: Protein/peptide | Mass: 849.865 Da / Num. of mol.: 1 / Fragment: unp residues 371-377 / Source method: obtained synthetically / Details: peptidyl boronic acid inhibitor / References: UniProt: Q80X68, UniProt: Q9CZU6*PLUS |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.41 Å3/Da / Density % sol: 63.89 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 1.0M LiSO4, 0.1M Sodium citrate, 0.5M (NH4)2SO4, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 292K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Sep 21, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9102 Å / Relative weight: 1 |
Reflection | Resolution: 2.75→25 Å / Num. all: 12884 / Num. obs: 12884 / % possible obs: 99.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Biso Wilson estimate: 81.4 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 11.3 |
Reflection shell | Resolution: 2.75→2.9 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.463 / Mean I/σ(I) obs: 2.8 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1LCY Resolution: 2.75→20 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.919 / SU B: 8.965 / SU ML: 0.187 / Cross valid method: THROUGHOUT / ESU R Free: 0.255 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 67.371 Å2
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Refinement step | Cycle: LAST / Resolution: 2.75→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.75→2.82 Å / Total num. of bins used: 20
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