+Open data
-Basic information
Entry | Database: PDB / ID: 2uuj | ||||||
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Title | Thrombin-hirugen-gw473178 ternary complex at 1.32A resolution | ||||||
Components |
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Keywords | HYDROLASE/HYDROLASE INHIBITOR / BLOOD CLOTTING / GLYCOPROTEIN / SERINE PROTEASE / SERINE PROTEASE INHIBITOR / HIRUGEN / ZYMOGEN / THROMBIN / PROTEASE / SULFATION / HIGH RESOLUTION / SERINE PROTEINASE / BLOOD COAGULATION / PROTEASE INHIBITOR / NON-COVALENT ACTIVE SITE INHIBITOR / 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 / 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 / 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 / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.32 Å | ||||||
Authors | Ahmed, H.U. / Blakeley, M.P. / Cianci, M. / Cruickshank, D.W.J. / Hubbard, J.A. / Helliwell, J.R. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2007 Title: The Determination of Protonation States in Proteins. Authors: Ahmed, H.U. / Blakeley, M.P. / Cianci, M. / Cruickshank, D.W.J. / Hubbard, J.A. / Helliwell, J.R. | ||||||
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 | 2uuj.cif.gz | 154.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2uuj.ent.gz | 120.2 KB | Display | PDB format |
PDBx/mmJSON format | 2uuj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2uuj_validation.pdf.gz | 766.7 KB | Display | wwPDB validaton report |
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Full document | 2uuj_full_validation.pdf.gz | 776.2 KB | Display | |
Data in XML | 2uuj_validation.xml.gz | 18.6 KB | Display | |
Data in CIF | 2uuj_validation.cif.gz | 27.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uu/2uuj ftp://data.pdbj.org/pub/pdb/validation_reports/uu/2uuj | HTTPS FTP |
-Related structure data
Related structure data | 2uu8C 2uufSC 2uukC 2yz4C C: citing same article (ref.) S: Starting model for refinement |
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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 AH
#1: Protein/peptide | Mass: 4096.534 Da / Num. of mol.: 1 / Fragment: 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: RESIDUES 55-64 / Source method: obtained synthetically Details: THIS POLYPEPTIDE CHAIN WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE FOR THIS CHAIN OCCURS NATURALLY IN THE C-TERMINAL OF MEDICINAL LEECH(HIRUDO MEDICINALIS). Source: (synth.) HIRUDO MEDICINALIS (medicinal leech) / References: UniProt: P28501, UniProt: P01050*PLUS |
-Protein , 1 types, 1 molecules B
#2: Protein | Mass: 29780.219 Da / Num. of mol.: 1 / Fragment: 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 , 4 types, 340 molecules
#4: Chemical | ChemComp-NA / |
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#5: Chemical | ChemComp-CA / |
#6: Chemical | ChemComp-896 / |
#7: Water | ChemComp-HOH / |
-Details
Has protein modification | Y |
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Sequence details | RESIDUES THAT ARE MISSING FROM CHAIN A ARE THR1H-ALA1B AND ARG15 RESIDUES THAT ARE MISSING FROM ...RESIDUES THAT ARE MISSING FROM CHAIN A ARE THR1H-ALA1B AND ARG15 RESIDUES THAT ARE MISSING FROM CHAIN B ARE THR147-THR149 |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 46.9 % Description: STARTING MODEL IS A THROMBIN-HIRUGEN BINARY COMPLEX |
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Crystal grow | pH: 7 Details: CRYSTALLIZATION CONDITIONS: CRYSTALS WERE GROWN BY MACROSEEDING A SOLUTION OF 100MM HEPES PH 7.0, 28% PEG4K, 500MM NACL. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX10.1 / Wavelength: 1.37 |
Detector | Type: MARRESEARCH / Detector: CCD |
Radiation | Monochromator: SI (1,1,1) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.37 Å / Relative weight: 1 |
Reflection | Resolution: 1.32→35.78 Å / Num. obs: 71295 / % possible obs: 86.9 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 12.75 |
Reflection shell | Resolution: 1.32→1.39 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2.32 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2UUF Resolution: 1.32→35.78 Å / Num. parameters: 25014 / Num. restraintsaints: 30856 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER Details: ASN60G IN CHAIN B IS GLYCOSYLATED. THE COORDINATES LIST BELOW HAS AMINO ACID NUMBERING FOLLOWING THE CHYMOTRYPSINOGEN NUMBERING SCHEME I.E. A MIXTURE OF SEQUENTIAL NUMBERS AND ALPHABETICAL ...Details: ASN60G IN CHAIN B IS GLYCOSYLATED. THE COORDINATES LIST BELOW HAS AMINO ACID NUMBERING FOLLOWING THE CHYMOTRYPSINOGEN NUMBERING SCHEME I.E. A MIXTURE OF SEQUENTIAL NUMBERS AND ALPHABETICAL LETTERS. ASN60G IN CHAIN B IS GLYCOSYLATED. THE MODEL WAS REFINED AGAINST F IN REFMAC-5, THEN FINALLY REFINED IN SHELXL-97. HYDROGENS HAVE BEEN ADDED IN RIDING POSITIONS.
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Refine analyze | Num. disordered residues: 14 / Occupancy sum hydrogen: 2289 / Occupancy sum non hydrogen: 2720.52 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.32→35.78 Å
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Refine LS restraints |
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