+Open data
-Basic information
Entry | Database: PDB / ID: 1toc | ||||||
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Title | STRUCTURE OF SERINE PROTEINASE | ||||||
Components |
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Keywords | COMPLEX (HYDROLASE/INHIBITOR) / VITAMIN K / ZYMOGEN / GAMMA-CARBOXYGLUTAMIC ACID / ACUTE PHASE / LIVER / HYDROLASE / SERINE PROTEASE KUNITZ-LIKE INHIBITOR / KRINGLE / COMPLEX (HYDROLASE-INHIBITOR) COMPLEX | ||||||
Function / homology | Function and homology information fibrinogen binding / thrombin / protein polymerization / positive regulation of blood coagulation / acute-phase response / platelet activation / serine-type endopeptidase inhibitor activity / collagen-containing extracellular matrix / serine-type endopeptidase activity / calcium ion binding ...fibrinogen binding / thrombin / protein polymerization / positive regulation of blood coagulation / acute-phase response / platelet activation / serine-type endopeptidase inhibitor activity / collagen-containing extracellular matrix / serine-type endopeptidase activity / calcium ion binding / proteolysis / extracellular space Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) Ornithodoros moubata (arthropod) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 3.1 Å | ||||||
Authors | Van De Locht, A. / Huber, R. / Bode, W. | ||||||
Citation | Journal: EMBO J. / Year: 1996 Title: The ornithodorin-thrombin crystal structure, a key to the TAP enigma? Authors: van de Locht, A. / Stubbs, M.T. / Bode, W. / Friedrich, T. / Bollschweiler, C. / Hoffken, W. / Huber, R. #1: Journal: Embo J. / Year: 1995 Title: Two Heads are Better Than One: Crystal Structure of the Insect Derived Double Domain Kazal Inhibitor Rhodniin in Complex with Thrombin Authors: Van De Locht, A. / Lamba, D. / Bauer, M. / Huber, R. / Friedrich, T. / Kroger, B. / Hoffken, W. / Bode, W. #2: Journal: Embo J. / Year: 1989 Title: The Refined 1.9 A Crystal Structure of Human Alpha-Thrombin: Interaction with D-Phe-Pro-Arg Chloromethylketone and Significance of the Tyr-Pro-Pro-Trp Insertion Segment Authors: Bode, W. / Mayr, I. / Baumann, U. / Huber, R. / Stone, S.R. / Hofsteenge, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1toc.cif.gz | 329.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1toc.ent.gz | 278.3 KB | Display | PDB format |
PDBx/mmJSON format | 1toc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/to/1toc ftp://data.pdbj.org/pub/pdb/validation_reports/to/1toc | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein/peptide | Mass: 5735.240 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Tissue: PLASMA / Plasmid: PMD8A / Production host: Escherichia coli (E. coli) / References: UniProt: P00735, thrombin #2: Protein | Mass: 29772.422 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Tissue: PLASMA / Plasmid: PMD8A / Production host: Escherichia coli (E. coli) / References: UniProt: P00735, thrombin #3: Protein | Mass: 12726.731 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ornithodoros moubata (arthropod) / Plasmid: PMD8A / Production host: Escherichia coli (E. coli) / References: UniProt: P56409 #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.81 Å3/Da / Density % sol: 56 % | |||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 20 ℃ / pH: 5 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Wavelength: 1.5418 |
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Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 13, 1996 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Num. obs: 94484 / % possible obs: 89 % / Observed criterion σ(I): 3 / Redundancy: 2.39 % / Rmerge(I) obs: 0.14 |
Reflection | *PLUS Highest resolution: 3 Å / Lowest resolution: 9999 Å |
Reflection shell | *PLUS Highest resolution: 3 Å / Lowest resolution: 3.13 Å / % possible obs: 75.2 % |
-Processing
Software |
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Refinement | Resolution: 3.1→10 Å / σ(F): 2 /
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Refinement step | Cycle: LAST / Resolution: 3.1→10 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |