[English] 日本語
![](img/lk-miru.gif)
- PDB-5hvh: Crystal Structure of Thrombin-activatable Fibrinolysis Inhibitor ... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 5hvh | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal Structure of Thrombin-activatable Fibrinolysis Inhibitor in Complex with two Inhibitory Nanobodies | |||||||||
![]() |
| |||||||||
![]() | HYDROLASE/HYDROLASE INHIBITOR / procarboxypeptidase U / thrombin-activatable fibrinolysis inhibitor / TAFI / procarboxypeptidase R / plasma procarboxypeptidase B / nanobody / antibody fragment / protein complex / HYDROLASE-HYDROLASE INHIBITOR complex | |||||||||
Function / homology | ![]() carboxypeptidase U / positive regulation of extracellular matrix constituent secretion / negative regulation of hepatocyte proliferation / negative regulation of plasminogen activation / negative regulation of fibrinolysis / metallocarboxypeptidase activity / Metabolism of Angiotensinogen to Angiotensins / fibrinolysis / Regulation of Complement cascade / liver regeneration ...carboxypeptidase U / positive regulation of extracellular matrix constituent secretion / negative regulation of hepatocyte proliferation / negative regulation of plasminogen activation / negative regulation of fibrinolysis / metallocarboxypeptidase activity / Metabolism of Angiotensinogen to Angiotensins / fibrinolysis / Regulation of Complement cascade / liver regeneration / cellular response to glucose stimulus / protein catabolic process / blood coagulation / response to xenobiotic stimulus / proteolysis / extracellular space / zinc ion binding / extracellular exosome / extracellular region Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() ![]() | |||||||||
![]() | Zhou, X. / Weeks, S.D. / Strelkov, S.V. / Declerck, P.J. | |||||||||
Funding support | ![]()
| |||||||||
![]() | ![]() Title: Elucidation of the molecular mechanisms of two nanobodies that inhibit thrombin-activatable fibrinolysis inhibitor activation and activated thrombin-activatable fibrinolysis inhibitor activity. Authors: Zhou, X. / Weeks, S.D. / Ameloot, P. / Callewaert, N. / Strelkov, S.V. / Declerck, P.J. | |||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 271.5 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 221.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 23.7 KB | Display | |
Data in CIF | ![]() | 32.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5hvfC ![]() 5hvgC ![]() 4p10S C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
-Protein , 2 types, 2 molecules AC
#1: Protein | Mass: 46080.176 Da / Num. of mol.: 1 / Mutation: S305C-T325I-T329I-H333Y-S335Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
---|---|
#3: Protein | Mass: 13706.022 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
-Antibody / Non-polymers , 2 types, 2 molecules B![](data/chem/img/ZN.gif)
![](data/chem/img/ZN.gif)
#2: Antibody | Mass: 14034.362 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
---|---|
#6: Chemical | ChemComp-ZN / |
-Sugars , 2 types, 4 molecules ![](data/chem/img/NAG.gif)
#4: Polysaccharide | Source method: isolated from a genetically manipulated source #5: Sugar | ChemComp-NAG / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 5.6 Å3/Da / Density % sol: 78.02 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 0.1 M sodium acetate trihydrate, 3.0 M sodium chloride |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 7, 2014 / Details: Kirkpatrick-Baez pair of bi-morph mirrors | ||||||||||||||||||||||||||||||
Radiation | Monochromator: channel cut cryogenically cooled monochromator crystal Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9801 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 3→49.25 Å / Num. obs: 34292 / % possible obs: 100 % / Redundancy: 21.9 % / Biso Wilson estimate: 69.68 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.266 / Rpim(I) all: 0.058 / Rrim(I) all: 0.272 / Net I/σ(I): 11.6 / Num. measured all: 750979 / Scaling rejects: 1018 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
|
-Phasing
Phasing | Method: ![]() |
---|
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 4P10 Resolution: 3→49.25 Å / Cor.coef. Fo:Fc: 0.8864 / Cor.coef. Fo:Fc free: 0.88 / SU R Cruickshank DPI: 0.349 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.342 / SU Rfree Blow DPI: 0.231 / SU Rfree Cruickshank DPI: 0.235
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 192.87 Å2 / Biso mean: 79.25 Å2 / Biso min: 23.5 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.372 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3→49.25 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 3→3.09 Å / Total num. of bins used: 17
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|