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Yorodumi- PDB-2ant: THE 2.6 A STRUCTURE OF ANTITHROMBIN INDICATES A CONFORMATIONAL CH... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ant | ||||||
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Title | THE 2.6 A STRUCTURE OF ANTITHROMBIN INDICATES A CONFORMATIONAL CHANGE AT THE HEPARIN BINDING SITE | ||||||
Components | ANTITHROMBIN | ||||||
Keywords | SERPIN / HEPARIN / INHIBITOR | ||||||
Function / homology | Function and homology information regulation of blood coagulation / Common Pathway of Fibrin Clot Formation / Intrinsic Pathway of Fibrin Clot Formation / Post-translational protein phosphorylation / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / serine-type endopeptidase inhibitor activity / blood coagulation / heparin binding / protease binding / collagen-containing extracellular matrix ...regulation of blood coagulation / Common Pathway of Fibrin Clot Formation / Intrinsic Pathway of Fibrin Clot Formation / Post-translational protein phosphorylation / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / serine-type endopeptidase inhibitor activity / blood coagulation / heparin binding / protease binding / collagen-containing extracellular matrix / blood microparticle / endoplasmic reticulum lumen / extracellular space / extracellular exosome / extracellular region / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Skinner, R. / Abrahams, J.-P. / Whisstock, J.C. / Lesk, A.M. / Carrell, R.W. / Wardell, M.R. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1997 Title: The 2.6 A structure of antithrombin indicates a conformational change at the heparin binding site. Authors: Skinner, R. / Abrahams, J.P. / Whisstock, J.C. / Lesk, A.M. / Carrell, R.W. / Wardell, M.R. #1: Journal: To be Published Title: Improved Diffraction of Antithrombin Crystals Grown in Microgravity Authors: Wardell, M.R. / Skinner, R. / Carter, D.C. / Twigg, P.D. / Abrahams, J.-P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ant.cif.gz | 170.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ant.ent.gz | 139.1 KB | Display | PDB format |
PDBx/mmJSON format | 2ant.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ant_validation.pdf.gz | 465.8 KB | Display | wwPDB validaton report |
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Full document | 2ant_full_validation.pdf.gz | 553.1 KB | Display | |
Data in XML | 2ant_validation.xml.gz | 42.8 KB | Display | |
Data in CIF | 2ant_validation.cif.gz | 56.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/an/2ant ftp://data.pdbj.org/pub/pdb/validation_reports/an/2ant | HTTPS FTP |
-Related structure data
Related structure data | 1antS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 49101.016 Da / Num. of mol.: 2 / Source method: isolated from a natural source Details: ANTITHROMBIN CRYSTALLISED AS A DIMER BETWEEN LATENT MOLECULE AND ONE ACTIVE MOLECULE Source: (natural) Homo sapiens (human) / Tissue: PLASMA / References: UniProt: P01008 #2: Sugar | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 52.7 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.7 / Details: 18% PEG 4000 50 MM NA/KPO4 PH 6.7 | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 8 / Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX7.2 / Wavelength: 1.488 |
Detector | Date: Apr 19, 1995 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.488 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→30 Å / Num. obs: 24646 / % possible obs: 74 % / Rmerge(I) obs: 0.048 |
Reflection shell | Resolution: 2.62→2.8 Å / % possible all: 53.9 |
Reflection | *PLUS Redundancy: 1.8 % |
Reflection shell | *PLUS % possible obs: 53.9 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1ANT Resolution: 2.6→26.9 Å / Cross valid method: RANDOM / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 2.6→26.9 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Version: 5D / Classification: refinement | ||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor all: 0.217 / Rfactor Rfree: 0.299 | ||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 2.64 Å / Lowest resolution: 2.72 Å / Rfactor Rfree: 0.63 / Rfactor obs: 0.37 |