+Open data
-Basic information
Entry | Database: PDB / ID: 1avg | ||||||
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Title | THROMBIN INHIBITOR FROM TRIATOMA PALLIDIPENNIS | ||||||
Components |
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Keywords | COMPLEX (BLOOD COAGULATION/INHIBITOR) / BOVINE THROMBIN / THROMBIN INHIBITOR / COMPLEX (BLOOD COAGULATION-INHIBITOR) / COMPLEX (BLOOD COAGULATION-INHIBITOR) complex | ||||||
Function / homology | Function and homology information symbiont-mediated perturbation of host defenses / fibrinogen binding / thrombin / protein polymerization / positive regulation of blood coagulation / acute-phase response / serine-type endopeptidase inhibitor activity / platelet activation / blood coagulation / collagen-containing extracellular matrix ...symbiont-mediated perturbation of host defenses / fibrinogen binding / thrombin / protein polymerization / positive regulation of blood coagulation / acute-phase response / serine-type endopeptidase inhibitor activity / platelet activation / blood coagulation / collagen-containing extracellular matrix / serine-type endopeptidase activity / calcium ion binding / proteolysis / extracellular space / extracellular region Similarity search - Function | ||||||
Biological species | Triatoma pallidipennis (insect) Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Fuentes-Prior, P. / Huber, R. / Bode, W. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 1997 Title: Structure of the thrombin complex with triabin, a lipocalin-like exosite-binding inhibitor derived from a triatomine bug. Authors: Fuentes-Prior, P. / Noeske-Jungblut, C. / Donner, P. / Schleuning, W.D. / Huber, R. / Bode, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1avg.cif.gz | 106 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1avg.ent.gz | 80.9 KB | Display | PDB format |
PDBx/mmJSON format | 1avg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1avg_validation.pdf.gz | 377.4 KB | Display | wwPDB validaton report |
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Full document | 1avg_full_validation.pdf.gz | 386.8 KB | Display | |
Data in XML | 1avg_validation.xml.gz | 11 KB | Display | |
Data in CIF | 1avg_validation.cif.gz | 17.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/av/1avg ftp://data.pdbj.org/pub/pdb/validation_reports/av/1avg | 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: 4792.293 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: BOVINE THROMBIN WAS PURIFIED FROM FROM FRESH OX BLOOD ACCORDING TO REPORTED PROTOCOLS Source: (natural) Bos taurus (cattle) / Organ: BLOOD / Secretion: BLOOD / Tissue: BLOOD / References: UniProt: P00735, thrombin |
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#2: Protein | Mass: 29772.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: BOVINE THROMBIN WAS PURIFIED FROM FROM FRESH OX BLOOD ACCORDING TO REPORTED PROTOCOLS Source: (natural) Bos taurus (cattle) / Organ: BLOOD / Secretion: BLOOD / Tissue: BLOOD / References: UniProt: P00735, thrombin |
#3: Protein | Mass: 16039.603 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Triatoma pallidipennis (insect) / Organ: BLOOD / Production host: INSECT CELLS / References: UniProt: Q27049 |
#4: Water | ChemComp-HOH / |
Compound details | ARG 15 A IS INSERTED IN THE ACTIVE SITE OF A NEIGHBORIN |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 4.6 Details: 50 MM NA ACETATE, PH 4.6, 100 MM (NH4)2SO4, 16 % PEG 4,000 | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 280 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 1, 1996 |
Radiation | Monochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→19.92 Å / Num. obs: 16392 / % possible obs: 93.2 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.099 / Rsym value: 0.112 / Net I/σ(I): 14.22 |
Reflection shell | Resolution: 2.6→2.67 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.121 / Mean I/σ(I) obs: 2.65 / Rsym value: 0.148 / % possible all: 81.6 |
Reflection | *PLUS Num. measured all: 79890 |
Reflection shell | *PLUS % possible obs: 81.6 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: BOVINE THROMBIN Resolution: 2.6→10 Å
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Refinement step | Cycle: LAST / Resolution: 2.6→10 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.842 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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