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Open data
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Basic information
Entry | Database: PDB / ID: 100000 | |||||||||
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Title | PLASMA ALPHA ANTITHROMBIN-III | |||||||||
![]() | ANTITHROMBIN-III | |||||||||
![]() | BLOOD CLOTTING / SERPIN | |||||||||
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 | ![]() ![]() ![]() | |||||||||
![]() | McCoy, A.J. / Skinner, R. / Abrahams, J.-P. / Pei, X.Y. / Carrell, R.W. | |||||||||
![]() | ![]() Title: Structure of Beta-Antithrombin and the Effect of Glycosylation on Antithrombin'S Heparin Affinity and Activity. Authors: Mccoy, A.J. / Pei, X.Y. / Skinner, R. / Abrahams, J.-P. / Carrell, R.W. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 184.6 KB | Display | ![]() |
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PDB format | ![]() | 145.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 740.9 KB | Display | ![]() |
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Full document | ![]() | 760.1 KB | Display | |
Data in XML | ![]() | 20.9 KB | Display | |
Data in CIF | ![]() | 30.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1e03C ![]() 1e04C ![]() 2antS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 2 molecules IL
#1: Protein | Mass: 49101.016 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: PLASMA ALPHA ANTITHROMBIN-III / Source: (natural) ![]() |
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-Sugars , 5 types, 11 molecules ![](data/chem/img/MAN.gif)
![](data/chem/img/NAG.gif)
![](data/chem/img/NAG.gif)
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...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 #4: Polysaccharide | beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose- ...beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[beta-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)]alpha-L-gulopyranose-(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: Sugar | #6: Sugar | ChemComp-NAG / |
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-Non-polymers , 3 types, 73 molecules ![](data/chem/img/GOL.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/HOH.gif)
#7: Chemical | #8: Chemical | ChemComp-PO4 / | #9: Water | ChemComp-HOH / | |
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-Details
Compound details | CHAIN I ADOPTS THE INHIBITORYSequence details | ANT3_HUMAN RESIDUE NUMBERING IS FROM START OF ANTITHROMBIN-III LEADER SEQUENCE. STRUCTURE RESIDUE ...ANT3_HUMAN RESIDUE NUMBERING IS FROM START OF ANTITHROMB | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.74 Å3/Da / Density % sol: 54 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.5 Details: CRYSTALS GROWN IN MICROGRAVITY NASA SPACE SHUTTLE MISSION STS-67 20MG/ML LATENT ANTITHROMBIN-III IN 20MM TRIS HCL PH 8.0 CRYSTALLIZED IN 19% PEG 4000, 50 MM NA/K PHOSPHATE PH 6.7, 0.05% AZIDE | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.4 / Method: unknown | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.488 Å / Relative weight: 1 |
Reflection | Resolution: 2.62→20 Å / Num. obs: 23397 / % possible obs: 72 % / Observed criterion σ(I): 0 / Redundancy: 1.8 % / Rmerge(I) obs: 0.048 |
Reflection | *PLUS Lowest resolution: 20 Å |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2ANT Resolution: 2.62→20 Å / SU B: 14.454 / SU ML: 0.29773 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.37082
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Displacement parameters | Biso mean: 53 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.62→20 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Num. reflection obs: 23397 / Num. reflection Rfree: 1351 / Rfactor obs: 0.207 / Rfactor Rfree: 0.258 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |