+
Open data
-
Basic information
Entry | Database: PDB / ID: 1t1f | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal Structure of Native Antithrombin in its Monomeric Form | |||||||||
![]() | Antithrombin-III | |||||||||
![]() | BLOOD CLOTTING / serine-cysteine proteinase inhibitor / thrombin / human / x-ray crystallography | |||||||||
Function / homology | ![]() regulation of blood coagulation / Common Pathway of Fibrin Clot Formation / Intrinsic Pathway of Fibrin Clot Formation / Post-translational protein phosphorylation / serine-type endopeptidase inhibitor activity / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / blood coagulation / heparin binding / collagen-containing extracellular matrix / protease binding ...regulation of blood coagulation / Common Pathway of Fibrin Clot Formation / Intrinsic Pathway of Fibrin Clot Formation / Post-translational protein phosphorylation / serine-type endopeptidase inhibitor activity / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / blood coagulation / heparin binding / collagen-containing extracellular matrix / protease binding / blood microparticle / endoplasmic reticulum lumen / extracellular space / extracellular exosome / extracellular region / identical protein binding / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Johnson, D.J.D. / Huntington, J.A. | |||||||||
![]() | ![]() Title: Crystal structure of monomeric native antithrombin reveals a novel reactive center loop conformation Authors: Johnson, D.J.D. / Langdown, J. / Li, W. / Luis, S.A. / Baglin, T.P. / Huntington, J.A. | |||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 265.6 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 213.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 3 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 3 MB | Display | |
Data in XML | ![]() | 59.6 KB | Display | |
Data in CIF | ![]() | 79.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2b5tC ![]() 2behC ![]() 1e04S S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||||
2 | ![]()
| ||||||||||
3 | ![]()
| ||||||||||
Unit cell |
|
-
Components
-Protein , 1 types, 3 molecules ABC
#1: Protein | Mass: 49091.066 Da / Num. of mol.: 3 / Mutation: S137A; V317C; T401C Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
---|
-Sugars , 2 types, 9 molecules
#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #3: Polysaccharide | Source method: isolated from a genetically manipulated source |
---|
-Non-polymers , 3 types, 240 molecules ![](data/chem/img/IOD.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-IOD / #5: Chemical | #6: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 51.9 % |
---|---|
Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: Sodium Iodide, PEG 3350, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 27, 2004 |
Radiation | Monochromator: single crystal Si monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 |
Reflection | Resolution: 2.75→38.52 Å / Num. all: 44339 / Num. obs: 44274 / % possible obs: 99.85 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 72.038 Å2 / Rmerge(I) obs: 0.112 / Rsym value: 0.112 / Net I/σ(I): 5.6 |
Reflection shell | Resolution: 2.75→2.9 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.512 / Mean I/σ(I) obs: 1.7 / Num. unique all: 10553 / Rsym value: 0.512 / % possible all: 71.8 |
-
Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB entry 1E04 Resolution: 2.75→38.46 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: Used strict NCS throughout using matrices: ( -0.499 0.002 0.866 ) ( -0.003 1.000 -0.004 ) ( -0.866 -0.004 -0.499 ) with translation ( 76.83844 29.37406 133.27936 ) for the second monomer, ...Details: Used strict NCS throughout using matrices: ( -0.499 0.002 0.866 ) ( -0.003 1.000 -0.004 ) ( -0.866 -0.004 -0.499 ) with translation ( 76.83844 29.37406 133.27936 ) for the second monomer, and ( -0.49880 0.00217 -0.86671 ) ( -0.00089 1.00000 0.00302 ) ( 0.86672 0.00228 -0.49880 ) with translation ( 153.71411 14.59701 -0.03036 ) for the third monomer.
| |||||||||||||||||||||||||
Displacement parameters | Biso mean: 59.7 Å2
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.75→38.46 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
LS refinement shell | Resolution: 2.75→2.92 Å / Rfactor Rfree error: 0.025
|