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- PDB-1ay6: THROMBIN INHIBITOR FROM THEONALLA, CYCLOTHEANAMIDE-BASED MACROCYC... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1ay6 | ||||||
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Title | THROMBIN INHIBITOR FROM THEONALLA, CYCLOTHEANAMIDE-BASED MACROCYCLIC TRIPEPTIDE MOTIF | ||||||
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![]() | HYDROLASE/HYDROLASE INHIBITOR / COMPLEX OF SERINE PROTEASE-INHIBITOR / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR COMPLEX | ||||||
Function / homology | ![]() 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 / fibrinolysis / regulation of cytosolic calcium ion concentration / 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 / serine-type endopeptidase inhibitor activity / positive regulation of insulin secretion / platelet activation / response to wounding / positive regulation of protein localization to nucleus / Golgi lumen / antimicrobial humoral immune response mediated by antimicrobial peptide / 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 / blood coagulation / Thrombin signalling through proteinase activated receptors (PARs) / heparin binding / regulation of cell shape / positive regulation of cell growth / G alpha (q) signalling events / collagen-containing extracellular matrix / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell surface receptor signaling pathway / blood microparticle / positive regulation of protein phosphorylation / G protein-coupled receptor signaling pathway / endoplasmic reticulum lumen / serine-type endopeptidase activity / signaling receptor binding / calcium ion binding / positive regulation of cell population proliferation / proteolysis / extracellular space / extracellular exosome / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Ganesh, V. / Maryanoff, B.E. / Tulinsky, A. | ||||||
![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 77.6 KB | Display | ![]() |
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PDB format | ![]() | 58.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 477.9 KB | Display | ![]() |
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Full document | ![]() | 509.1 KB | Display | |
Data in XML | ![]() | 13 KB | Display | |
Data in CIF | ![]() | 18.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1tmbSC 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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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein/peptide | Mass: 4096.534 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#2: Protein | Mass: 29780.219 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#3: Protein/peptide | Mass: 1632.654 Da / Num. of mol.: 1 / Fragment: residues 55-64 / Source method: obtained synthetically / Details: Acetyl hirugen / Source: (synth.) ![]() |
#4: Chemical | ChemComp-1ZV / ![]() 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: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 51 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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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
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-Data collection
Diffraction | Mean temperature: 300 K |
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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 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1TMB Resolution: 1.8→7 Å / Cross valid method: THROUGHOUT / σ(F): 4
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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
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Refine LS restraints |
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