+Open data
-Basic information
Entry | Database: PDB / ID: 1way | ||||||
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Title | Active site thrombin inhibitors | ||||||
Components |
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Keywords | HYDROLASE/HYDROLASE INHIBITOR / PROTEASE / BLOOD COAGULATION / ACUTE PHASE / CALCIUM-BINDING / DISEASE MUTATION / GAMMA-CARBOXYGLUTAMIC ACID / GLYCOPROTEIN / KRINGLE / PLASMA / SERINE PROTEASE / VITAMIN K / HYDROLASE-HYDROLASE INHIBITOR COMPLEX | ||||||
Function / homology | Function and homology information negative regulation of serine-type peptidase activity / positive regulation of lipid kinase activity / cytolysis by host of symbiont cells / positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / 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 / cytolysis by host of symbiont cells / positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / 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 / positive regulation of receptor signaling pathway via JAK-STAT / lipopolysaccharide binding / 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 / 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 / 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 / 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) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.02 Å | ||||||
Authors | Hartshorn, M.J. / Murray, C.W. / Cleasby, A. / Frederickson, M. / Tickle, I.J. / Jhoti, H. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2005 Title: Fragment-Based Lead Discovery Using X-Ray Crystallography Authors: Hartshorn, M.J. / Murray, C.W. / Cleasby, A. / Frederickson, M. / Tickle, I.J. / Jhoti, H. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "BB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "BB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET 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 | 1way.cif.gz | 89.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1way.ent.gz | 66.7 KB | Display | PDB format |
PDBx/mmJSON format | 1way.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1way_validation.pdf.gz | 454.1 KB | Display | wwPDB validaton report |
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Full document | 1way_full_validation.pdf.gz | 455 KB | Display | |
Data in XML | 1way_validation.xml.gz | 7.6 KB | Display | |
Data in CIF | 1way_validation.cif.gz | 13.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wa/1way ftp://data.pdbj.org/pub/pdb/validation_reports/wa/1way | HTTPS FTP |
-Related structure data
Related structure data | 1w7hC 1waxC 1wbgC 1wboC 1wbuC 1wccC 1qj1S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein/peptide , 2 types, 2 molecules AI
#1: Protein/peptide | Mass: 4096.534 Da / Num. of mol.: 1 / Fragment: FRAGMENT ALPHA THROMBIN, RESIDUES 328-363 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Tissue: BLOOD PLASMA / References: UniProt: P00734, thrombin |
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#3: Protein/peptide | Mass: 1363.399 Da / Num. of mol.: 1 / Fragment: PEPTIDE FRAGMENT OF HIRUGEN, RESIDUES 62-71 / Source method: obtained synthetically / Source: (synth.) HIRUDO MEDICINALIS (medicinal leech) / References: UniProt: P01050*PLUS |
-Protein , 1 types, 1 molecules B
#2: Protein | Mass: 29780.219 Da / Num. of mol.: 1 / Fragment: FRAGMENT ALPHA THROMBIN, RESIDUES 364-622 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Tissue: BLOOD PLASMA / References: UniProt: P00734, thrombin |
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-Non-polymers , 3 types, 395 molecules
#4: Chemical | ChemComp-L02 / | ||
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#5: Chemical | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.54 Å3/Da / Density % sol: 51.57 % |
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Crystal grow | pH: 7.3 / Details: PH 7.30 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.54 |
Detector | Type: RIGAKU CCD / Detector: CCD / Date: Nov 6, 2002 / Details: CONFOCAL MULTILAYER |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2→71 Å / Num. obs: 23016 / % possible obs: 97.7 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 2.7 |
Reflection shell | Resolution: 2.02→2.07 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 3 / % possible all: 99.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1QJ1 Resolution: 2.02→49.78 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.918 / SU B: 4.159 / SU ML: 0.115 / Cross valid method: THROUGHOUT / ESU R: 0.17 / ESU R Free: 0.172 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDER AT TWO-FOLD; ARG B 75 CLASHES. THE OCCUPANCY OF SIDE CHAIN ATOMS WAS SET TO 0 FOR REFINEMENT. THESE ATOMS REMOVED FOR DURING PDB ANNOTATION.
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.37 Å2
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Refinement step | Cycle: LAST / Resolution: 2.02→49.78 Å
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Refine LS restraints |
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