[English] 日本語
Yorodumi- PDB-1ay6: THROMBIN INHIBITOR FROM THEONALLA, CYCLOTHEANAMIDE-BASED MACROCYC... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ay6 | ||||||
---|---|---|---|---|---|---|---|
Title | THROMBIN INHIBITOR FROM THEONALLA, CYCLOTHEANAMIDE-BASED MACROCYCLIC TRIPEPTIDE MOTIF | ||||||
Components |
| ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / COMPLEX OF SERINE PROTEASE-INHIBITOR / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR COMPLEX | ||||||
Function / homology | Function and homology information negative regulation of serine-type peptidase activity / positive regulation of lipid kinase activity / positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / cytolysis by host of symbiont cells / thrombospondin receptor activity / Defective factor XII causes hereditary angioedema / thrombin / regulation of blood coagulation / neutrophil-mediated killing of gram-negative bacterium / ligand-gated ion channel signaling pathway ...negative regulation of serine-type peptidase activity / positive regulation of lipid kinase activity / positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / cytolysis by host of symbiont cells / thrombospondin receptor activity / Defective factor XII causes hereditary angioedema / thrombin / regulation of blood coagulation / neutrophil-mediated killing of gram-negative bacterium / ligand-gated ion channel signaling pathway / Defective F8 cleavage by thrombin / Platelet Aggregation (Plug Formation) / negative regulation of astrocyte differentiation / negative regulation of platelet activation / positive regulation of collagen biosynthetic process / negative regulation of cytokine production involved in inflammatory response / positive regulation of blood coagulation / negative regulation of fibrinolysis / Gamma-carboxylation of protein precursors / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / Common Pathway of Fibrin Clot Formation / Removal of aminoterminal propeptides from gamma-carboxylated proteins / regulation of cytosolic calcium ion concentration / fibrinolysis / Intrinsic Pathway of Fibrin Clot Formation / Peptide ligand-binding receptors / positive regulation of release of sequestered calcium ion into cytosol / acute-phase response / Regulation of Complement cascade / negative regulation of proteolysis / Cell surface interactions at the vascular wall / lipopolysaccharide binding / positive regulation of receptor signaling pathway via JAK-STAT / growth factor activity / positive regulation of insulin secretion / platelet activation / response to wounding / positive regulation of protein localization to nucleus / Golgi lumen / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / positive regulation of reactive oxygen species metabolic process / serine-type endopeptidase inhibitor activity / antimicrobial humoral immune response mediated by antimicrobial peptide / blood coagulation / Thrombin signalling through proteinase activated receptors (PARs) / heparin binding / positive regulation of cell growth / regulation of cell shape / G alpha (q) signalling events / collagen-containing extracellular matrix / blood microparticle / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell surface receptor signaling pathway / positive regulation of protein phosphorylation / G protein-coupled receptor signaling pathway / endoplasmic reticulum lumen / serine-type endopeptidase activity / signaling receptor binding / positive regulation of cell population proliferation / calcium ion binding / proteolysis / extracellular space / extracellular exosome / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Hirudo medicinalis (medicinal leech) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Ganesh, V. / Maryanoff, B.E. / Tulinsky, A. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 1996 Title: Novel thrombin inhibitors that are based on a macrocyclic tripeptide motif Authors: Greco, M.N. / Powell, E.T. / Hecker, L.R. / Andrade-Gordon, P. / Kauffman, J.A. / Lewis, J.M. / Ganesh, V. / Tulinsky, A. / Maryanoff, B.E. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1ay6.cif.gz | 77.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1ay6.ent.gz | 58.4 KB | Display | PDB format |
PDBx/mmJSON format | 1ay6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ay6_validation.pdf.gz | 477.9 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1ay6_full_validation.pdf.gz | 509.1 KB | Display | |
Data in XML | 1ay6_validation.xml.gz | 13 KB | Display | |
Data in CIF | 1ay6_validation.cif.gz | 18.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ay/1ay6 ftp://data.pdbj.org/pub/pdb/validation_reports/ay/1ay6 | HTTPS FTP |
-Related structure data
Related structure data | 1tmbSC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-Components
#1: Protein/peptide | Mass: 4096.534 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Tissue: BLOOD / References: UniProt: P00734, thrombin |
---|---|
#2: Protein | Mass: 29780.219 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Tissue: BLOOD / References: UniProt: P00734, thrombin |
#3: Protein/peptide | Mass: 1632.654 Da / Num. of mol.: 1 / Fragment: residues 55-64 / Source method: obtained synthetically / Details: Acetyl hirugen / Source: (synth.) Hirudo medicinalis (medicinal leech) / References: UniProt: P01050 |
#4: Chemical | ChemComp-1ZV / Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 588.762 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H50N7O5 References: amino({3-[(3R,5R,14S,16S,21aR)-5,14-dihydroxy-1,4,17-trioxo-16-(2-phenylethyl)icosahydro-1H-pyrrolo[1,2-d][1,4,7,11]tetraazacyclononadecin-3-yl]propyl}amino)methaniminium |
#5: Water | ChemComp-HOH / |
Nonpolymer details | THE CYCLIC LIGAND 1ZV COVALENTLY BINDS TO THROMBIN HEAVY CHAIN BETWEEN C8 ATOM OF 1ZV5H AND OG ATOM ...THE CYCLIC LIGAND 1ZV COVALENTLY |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 51 % | ||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 7.5 Details: CRYSTALLIZED FROM 25% PEG 8K, 0.1M SOD. PHOSPHATE BUFFER PH 7.5. MACROSEEDED TO MAKE LARGER CRYSTALS | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop / Details: Skrzypczak, J., (1991) J. Mol. Biol., 221, 1379. / pH: 7.3 | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 300 K |
---|---|
Diffraction source | Wavelength: 1.5418 |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Aug 15, 1993 |
Radiation | Monochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Highest resolution: 1.8 Å / Num. obs: 25408 / % possible obs: 74 % / Observed criterion σ(I): 2.5 / Redundancy: 2.5 % / Rmerge(I) obs: 0.045 / Rsym value: 0.12 / Net I/σ(I): 14 |
Reflection shell | Resolution: 1.8→2 Å / Redundancy: 2 % / Rmerge(I) obs: 0.06 / Mean I/σ(I) obs: 2.5 / Rsym value: 0.25 / % possible all: 65 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1TMB Resolution: 1.8→7 Å / Cross valid method: THROUGHOUT / σ(F): 4
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.2 Å / Luzzati d res low obs: 7 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→7 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|