+Open data
-Basic information
Entry | Database: PDB / ID: 3hat | ||||||||||||
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Title | ACTIVE SITE MIMETIC INHIBITION OF THROMBIN | ||||||||||||
Components |
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Keywords | HYDROLASE/HYDROLASE INHIBITOR / COMPLEX (SERINE PROTEASE-INHIBITOR) / COMPLEX (SERINE PROTEASE-INHIBITOR) complex / HYDROLASE-HYDROLASE INHIBITOR COMPLEX | ||||||||||||
Function / homology | Function and homology information 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 / neutrophil-mediated killing of gram-negative bacterium / regulation of blood coagulation / ligand-gated ion channel signaling pathway / Defective F8 cleavage by thrombin ...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 / neutrophil-mediated killing of gram-negative bacterium / regulation of blood coagulation / ligand-gated ion channel signaling pathway / Defective F8 cleavage by thrombin / Platelet Aggregation (Plug Formation) / negative regulation of platelet activation / negative regulation of astrocyte differentiation / 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 / Regulation of Complement cascade / acute-phase response / Cell surface interactions at the vascular wall / lipopolysaccharide binding / negative regulation of proteolysis / 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 / Golgi lumen / positive regulation of protein localization to nucleus / 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 / antimicrobial humoral immune response mediated by antimicrobial peptide / 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 / blood microparticle / cell surface receptor signaling pathway / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of protein phosphorylation / G protein-coupled receptor signaling pathway / endoplasmic reticulum lumen / signaling receptor binding / serine-type endopeptidase activity / calcium ion binding / positive regulation of cell population proliferation / proteolysis / extracellular space / extracellular exosome / extracellular region / plasma membrane Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) Hirudo medicinalis (medicinal leech) synthetic construct (others) | ||||||||||||
Method | X-RAY DIFFRACTION / Resolution: 2.5 Å | ||||||||||||
Authors | Tulinsky, A. / Mathews, I.I. | ||||||||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 1995 Title: Active-site mimetic inhibition of thrombin. Authors: Mathews, I.I. / Tulinsky, A. #1: Journal: Protein Eng. / Year: 1993 Title: The Structure of a Designed Peptidomimetic Inhibitor Complex of Alpha-Thrombin Authors: Wu, T.-P. / Yee, V. / Tulinsky, A. / Chrusciel, R.A. / Nakanishi, H. / Shen, R. / Priebe, C. / Kahn, M. #2: Journal: Blood Coagulation Fibrinolysis / Year: 1993 Title: Active Site and Exosite Binding of Alpha-Thrombin Authors: Tulinsky, A. / Qiu, X. #3: Journal: Biochemistry / Year: 1979 Title: Interactions of a Fluorescent Active-Site-Directed Inhibitor of Thrombin: Dansylarginine N-(3-Ethyl-1,5-Pentanediyl)Amide Authors: Nesheim, M.E. / Prendergast, F.G. / Mann, K.G. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3hat.cif.gz | 81 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3hat.ent.gz | 58.6 KB | Display | PDB format |
PDBx/mmJSON format | 3hat.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ha/3hat ftp://data.pdbj.org/pub/pdb/validation_reports/ha/3hat | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Atom site foot note | 1: CIS PROLINE - PRO H 37 | ||||||||
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) Homo sapiens (human) / Organ: BLOOD / Tissue: BLOOD / References: UniProt: P00734 |
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#2: Protein | Mass: 29780.219 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Organ: BLOOD / Tissue: BLOOD / References: UniProt: P00734 |
#3: Protein/peptide | Mass: 1534.554 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Hirudo medicinalis (medicinal leech) / References: UniProt: P09945 |
#4: Protein/peptide | Mass: 537.632 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: The capping residue of FPAM is not fully modeled. The SMILES string of the capping residue is OC(=O)C[C@H]1CCCN2N1C(=O)C(CCC2=O)C(NCC1=CC=CC=C1)C1=CC=CC=C1 Source: (synth.) synthetic construct (others) |
#5: Water | ChemComp-HOH / |
Compound details | THROMBIN IS CLEAVED BETWEEN RESIDUES 15 AND 16. CHAIN IDENTIFIER *L* IS USED FOR RESIDUES 1H - 15 ...THROMBIN IS CLEAVED BETWEEN RESIDUES 15 AND 16. CHAIN IDENTIFIER |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.56 Å3/Da / Density % sol: 51.89 % |
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Crystal grow | *PLUS Method: other / Details: Wu, T.P., (1993) Protein Eng., 6, 471. |
-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 2.5 Å / Num. obs: 22675 / Num. measured all: 37533 / Rmerge(I) obs: 0.039 |
-Processing
Software | Name: PROLSQ / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Rfactor obs: 0.14 / Highest resolution: 2.5 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 2.5 Å
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Refine LS restraints |
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Refinement | *PLUS Rfactor obs: 0.14 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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