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- PDB-4bxs: Crystal Structure of the Prothrombinase Complex from the Venom of... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4bxs | |||||||||
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Title | Crystal Structure of the Prothrombinase Complex from the Venom of Pseudonaja Textilis | |||||||||
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![]() | BLOOD CLOTTING / BLOOD COAGULATION / PROTHROMBINASE / HYDROLASE | |||||||||
Function / homology | ![]() induction of blood coagulation in another organism / envenomation resulting in positive regulation of blood coagulation in another organism / peptidase activator activity / coagulation factor Xa / blood coagulation / toxin activity / copper ion binding / serine-type endopeptidase activity / calcium ion binding / protein-containing complex ...induction of blood coagulation in another organism / envenomation resulting in positive regulation of blood coagulation in another organism / peptidase activator activity / coagulation factor Xa / blood coagulation / toxin activity / copper ion binding / serine-type endopeptidase activity / calcium ion binding / protein-containing complex / proteolysis / extracellular region Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Lechtenberg, B.C. / Murray-Rust, T.A. / Johnson, D.J.D. / Adams, T.E. / Krishnaswamy, S. / Camire, R.M. / Huntington, J.A. | |||||||||
![]() | ![]() Title: Crystal Structure of the Prothrombinase Complex from the Venom of Pseudonaja Textilis. Authors: Lechtenberg, B.C. / Murray-Rust, T.A. / Johnson, D.J. / Adams, T.E. / Krishnaswamy, S. / Camire, R.M. / Huntington, J.A. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 321.6 KB | Display | ![]() |
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PDB format | ![]() | 242.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.5 MB | Display | ![]() |
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Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 73.9 KB | Display | |
Data in CIF | ![]() | 98.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4bxwC ![]() 1kigS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 2 types, 2 molecules AV
#1: Protein | Mass: 47041.273 Da / Num. of mol.: 1 / Fragment: EGF2-CATALYTIC DOMAIN CONSTRUCT Source method: isolated from a genetically manipulated source Details: PSEUTARIN C CATALYTIC SUBUNIT Source: (gene. exp.) ![]() Organ: VENOM GLAND / Production host: ![]() ![]() |
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#2: Protein | Mass: 162826.781 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Organ: VENOM GLAND / Plasmid: PED / Cell line (production host): BHK-M / Production host: ![]() ![]() |
-Sugars , 4 types, 5 molecules ![](data/chem/img/NAG.gif)
#3: Polysaccharide | alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source | ||
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#4: Polysaccharide | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source | ||
#5: Polysaccharide | Source method: isolated from a genetically manipulated source #6: Sugar | ChemComp-NAG / | |
-Non-polymers , 3 types, 115 molecules ![](data/chem/img/CA.gif)
![](data/chem/img/CU.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CU.gif)
![](data/chem/img/HOH.gif)
#7: Chemical | #8: Chemical | ChemComp-CU / | #9: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.72 Å3/Da / Density % sol: 66.98 % / Description: NONE |
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Crystal grow | pH: 8 Details: 0.1 M MORPHEUS BUFFER 3, 20% MORPHEUS P20K_P550MME, 50 MM MORPHEUS CARBOXYLIC ACIDS, pH 8 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jul 21, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8856 Å / Relative weight: 1 |
Reflection | Resolution: 3.32→101.59 Å / Num. obs: 43913 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 6 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 7.8 |
Reflection shell | Resolution: 3.32→3.5 Å / Redundancy: 5.4 % / Rmerge(I) obs: 1 / Mean I/σ(I) obs: 1.5 / % possible all: 95.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: UNPUBLISHED FV STRUCTURE AND PDB ENTRY 1KIG Resolution: 3.32→89.81 Å / Cor.coef. Fo:Fc: 0.891 / Cor.coef. Fo:Fc free: 0.81 / SU B: 38.223 / SU ML: 0.605 / Cross valid method: THROUGHOUT / ESU R Free: 0.648 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED SIDE CHAINS AND LOOPS WERE NOT MODELLED, WITH THE EXCEPTION OF A PORTION OF THE A2-REGION OF FV (656-670)
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 117.583 Å2
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Refinement step | Cycle: LAST / Resolution: 3.32→89.81 Å
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Refine LS restraints |
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