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- PDB-3d4u: Bovine thrombin-activatable fibrinolysis inhibitor (TAFIa) in com... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3d4u | ||||||
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Title | Bovine thrombin-activatable fibrinolysis inhibitor (TAFIa) in complex with tick-derived carboxypeptidase inhibitor. | ||||||
![]() | (Carboxypeptidase ...) x 2 | ||||||
![]() | HYDROLASE/HYDROLASE INHIBITOR / protease-inhibitor complex / Carboxypeptidase / Glycoprotein / Hydrolase / Metal-binding / Metalloprotease / Protease / Secreted / Zymogen / Blood coagulation / Fibrinolysis / Metalloenzyme inhibitor / Metalloprotease inhibitor / HYDROLASE-HYDROLASE INHIBITOR COMPLEX | ||||||
Function / homology | ![]() Regulation of Complement cascade / Metabolism of Angiotensinogen to Angiotensins / carboxypeptidase U / acquisition of nutrients from host / metalloendopeptidase inhibitor activity / enzyme inhibitor activity / metallocarboxypeptidase activity / fibrinolysis / blood coagulation / toxin activity ...Regulation of Complement cascade / Metabolism of Angiotensinogen to Angiotensins / carboxypeptidase U / acquisition of nutrients from host / metalloendopeptidase inhibitor activity / enzyme inhibitor activity / metallocarboxypeptidase activity / fibrinolysis / blood coagulation / toxin activity / proteolysis / extracellular space / zinc ion binding / extracellular region Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Sanglas, L. / Valnickova, Z. / Arolas, J.L. / Pallares, I. / Guevara, T. / Sola, M. / Kristensen, T. / Enghild, J.J. / Aviles, F.X. / Gomis-Ruth, F.X. | ||||||
![]() | ![]() Title: Structure of activated thrombin-activatable fibrinolysis inhibitor, a molecular link between coagulation and fibrinolysis. Authors: Sanglas, L. / Valnickova, Z. / Arolas, J.L. / Pallares, I. / Guevara, T. / Sola, M. / Kristensen, T. / Enghild, J.J. / Aviles, F.X. / Gomis-Ruth, F.X. #1: ![]() Title: Human procarboxypeptidase B: three-dimensional structure and implications for thrombin-activatable fibrinolysis inhibitor (TAFI) Authors: Barbosa Pereira, P.J. / Oliva, B. / Ferrer-Orta, C. / Coll, M. / Vendrell, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 99.6 KB | Display | ![]() |
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PDB format | ![]() | 74.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 452.5 KB | Display | ![]() |
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Full document | ![]() | 454.6 KB | Display | |
Data in XML | ![]() | 19 KB | Display | |
Data in CIF | ![]() | 28.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1zliS 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
-Carboxypeptidase ... , 2 types, 2 molecules AB
#1: Protein | Mass: 36029.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#2: Protein | Mass: 7806.957 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-Non-polymers , 4 types, 366 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-ZN / | ||||
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#4: Chemical | #5: Chemical | ChemComp-SO4 / #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.98 Å3/Da / Density % sol: 58.67 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 0.2M (NH4)2SO4, 0.1M NaAcO, 10% PEG 4000, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Jul 18, 2007 Details: horizontally diffracting Si (111) monochromator and Pt coated mirrors in a Kirkpatrick-Baez (KB) geometry as the focusing system. |
Radiation | Monochromator: Horizontally diffracting Si (111) monochromator and Pt coated mirrors in a Kirkpatrick-Baez (KB) geometry as the focusing system Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→48.1 Å / Num. all: 62124 / Num. obs: 57962 / % possible obs: 93.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 15.1 % / Biso Wilson estimate: 18.6 Å2 / Rmerge(I) obs: 0.099 / Rsym value: 0.099 / Net I/σ(I): 20.6 |
Reflection shell | Resolution: 1.7→1.79 Å / Redundancy: 9.2 % / Rmerge(I) obs: 0.611 / Mean I/σ(I) obs: 9.2 / Num. unique all: 8032 / Rsym value: 0.611 / % possible all: 95.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1ZLI Resolution: 1.7→48.08 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.968 / SU B: 3.053 / SU ML: 0.046 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.074 / ESU R Free: 0.071 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.858 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→48.08 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.744 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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