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Yorodumi- PDB-1hdt: STRUCTURE OF A RETRO-BINDING PEPTIDE INHIBITOR COMPLEXED WITH HUM... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1hdt | ||||||
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Title | STRUCTURE OF A RETRO-BINDING PEPTIDE INHIBITOR COMPLEXED WITH HUMAN ALPHA-THROMBIN | ||||||
Components |
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Keywords | HYDROLASE/HYDROLASE INHIBITOR / SERINE PROTEINASE / 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 / regulation of blood coagulation / neutrophil-mediated killing of gram-negative bacterium / 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 / 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 | Hirudo medicinalis (medicinal leech) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.6 Å | ||||||
Authors | Tabernero, L. / Sack, J. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1995 Title: Structure of a retro-binding peptide inhibitor complexed with human alpha-thrombin. Authors: Tabernero, L. / Chang, C.Y. / Ohringer, S.L. / Lau, W.F. / Iwanowicz, E.J. / Han, W.C. / Wang, T.C. / Seiler, S.M. / Roberts, D.G. / Sack, J.S. | ||||||
History |
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Remark 700 | SHEET THE SHEETS PRESENTED AS B1 AND B2 ON SHEET RECORDS BELOW ACTUALLY COMPRISE SIX-STRANDED BETA- ...SHEET THE SHEETS PRESENTED AS B1 AND B2 ON SHEET RECORDS BELOW ACTUALLY COMPRISE SIX-STRANDED BETA-BARRELS. THESE ARE REPRESENTED BY SEVEN-STRANDED SHEETS IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1hdt.cif.gz | 78.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1hdt.ent.gz | 58.3 KB | Display | PDB format |
PDBx/mmJSON format | 1hdt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1hdt_validation.pdf.gz | 469.3 KB | Display | wwPDB validaton report |
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Full document | 1hdt_full_validation.pdf.gz | 487.8 KB | Display | |
Data in XML | 1hdt_validation.xml.gz | 10.5 KB | Display | |
Data in CIF | 1hdt_validation.cif.gz | 15.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hd/1hdt ftp://data.pdbj.org/pub/pdb/validation_reports/hd/1hdt | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein/peptide | Mass: 3791.204 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P00734, thrombin |
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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) / References: UniProt: P00734, thrombin |
#3: Protein/peptide | Mass: 1548.580 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Hirudo medicinalis (medicinal leech) / References: UniProt: P28507, UniProt: P28509*PLUS |
#4: Chemical | ChemComp-0E7 / |
#5: Water | ChemComp-HOH / |
Compound details | THROMBIN IS CLEAVED BETWEEN RESIDUES 15 AND 16. CHAIN INDICATOR *L* IS USED FOR RESIDUES 1H - 15. ...THROMBIN IS CLEAVED BETWEEN RESIDUES 15 AND 16. CHAIN INDICATOR *L* IS USED FOR RESIDUES 1H - 15. CHAIN INDICATOR *H* IS USED FOR RESIDUES 16 - 247. CHAIN INDICATOR *P* IS USED FOR THE HIRUGEN PEPTIDE. |
Nonpolymer details | THE INHIBITOR IS DESCRIBED AS A FOUR RESIDUE PSEUDO-PEPTIDE CONTAINING AN ALKYL-GUANIDINO GROUP ...THE INHIBITOR IS DESCRIBED AS A FOUR RESIDUE PSEUDO-PEPTIDE CONTAINING |
Sequence details | CHYMOTRYPSIN NUMBERING (RATHER THAN SEQUENTIAL) SYSTEM IS USED, BASED ON THE TOPOLOGICAL ALIGNMENT ...CHYMOTRYPS |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.86 Å3/Da / Density % sol: 56.97 % | |||||||||||||||||||||||||
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Crystal grow | *PLUS Method: vapor diffusion | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 2.6 Å / Num. obs: 11866 / % possible obs: 85 % / Observed criterion σ(I): 2 / Num. measured all: 22579 / Rmerge(I) obs: 0.079 |
-Processing
Software |
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Refinement | Resolution: 2.6→8 Å / σ(F): 2 /
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Refinement step | Cycle: LAST / Resolution: 2.6→8 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 2.6 Å / Lowest resolution: 6 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |