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Open data
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Basic information
Entry | Database: PDB / ID: 1oyh | |||||||||
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Title | Crystal Structure of P13 Alanine Variant of Antithrombin | |||||||||
![]() | (Antithrombin- ...) x 2 | |||||||||
![]() | BLOOD CLOTTING / thrombin / inhibition / heparin analogue / SERINE PROTEASE INHIBITOR | |||||||||
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: The influence of hinge region residue Glu-381 on antithrombin allostery and metastability Authors: Johnson, D.J.D. / 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 | ![]() | 179.1 KB | Display | ![]() |
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PDB format | ![]() | 140.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 35.8 KB | Display | |
Data in CIF | ![]() | 47.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1e04S 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
-Antithrombin- ... , 2 types, 2 molecules IL
#1: Protein | Mass: 49026.980 Da / Num. of mol.: 1 / Mutation: E381A, S137A Source method: isolated from a genetically manipulated source Details: E381A mutant on the beta glycoform background of S137A Source: (gene. exp.) ![]() Description: Plasma alpha antithrombin was converted to latent by the glycerol method, and is chain L Organ: blood / Plasmid: pMASTOP / Cell (production host): Baby Hampster Kidney Cells / Production host: ![]() ![]() |
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#2: Protein | Mass: 49101.016 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: beta glycoform / Source: (gene. exp.) ![]() Description: Plasma alpha antithrombin was converted to latent by the glycerol method, and is chain L Organ: blood / Plasmid: pMASTOP / Cell (production host): Baby Hampster Kidney Cells / Production host: ![]() ![]() |
-Sugars , 3 types, 7 molecules ![](data/chem/img/NAG.gif)
#3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Polysaccharide | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[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: Sugar | ChemComp-NAG / |
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-Non-polymers , 1 types, 54 molecules ![](data/chem/img/HOH.gif)
#6: Water | ChemComp-HOH / |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.14 Å3/Da / Density % sol: 60.5 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.7 Details: Na/K Phosphate, PEG 4000, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Detector: AREA DETECTOR |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.62→39.5 Å / Num. all: 36632 / Num. obs: 35267 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 6.1 % / Biso Wilson estimate: 76.609 Å2 / Rmerge(I) obs: 0.073 / Rsym value: 0.067 / Net I/σ(I): 9 |
Reflection shell | Resolution: 2.62→2.74 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.496 / Mean I/σ(I) obs: 3.2 / Num. unique all: 5109 / Rsym value: 0.453 / % possible all: 96.4 |
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Processing
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Refinement | Method to determine structure: ![]()
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Displacement parameters |
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.62→39 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.62→2.76 Å / Rfactor Rfree error: 0.023
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