+Open data
-Basic information
Entry | Database: PDB / ID: 2hij | |||||||||
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Title | Crystal Structure of P14 Alanine Variant of Antithrombin | |||||||||
Components | (Antithrombin- ...) x 2 | |||||||||
Keywords | BLOOD CLOTTING/ HYDROLASE INHIBITOR / THROMBIN / INHIBITION / HEPARIN ANALOGUE / SERINE PROTEASE 2 INHIBITOR / BLOOD CLOTTING- HYDROLASE INHIBITOR COMPLEX | |||||||||
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 / 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 | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | |||||||||
Authors | Luis, S.A. / Bock, S.C. / Huntington, J.A. | |||||||||
Citation | Journal: To be Published Title: Crystal Structure of P14 Alanine Variant of Antithrombin | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2hij.cif.gz | 173.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2hij.ent.gz | 134 KB | Display | PDB format |
PDBx/mmJSON format | 2hij.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hi/2hij ftp://data.pdbj.org/pub/pdb/validation_reports/hi/2hij | HTTPS FTP |
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-Related structure data
Related structure data | 1e04S 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
-Antithrombin- ... , 2 types, 2 molecules IL
#1: Protein | Mass: 49041.992 Da / Num. of mol.: 1 / Mutation: S380A, N135A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SERPINC1, AT3 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: P01008 |
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#2: Protein | Mass: 49101.016 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: alpha glycoform, plasma alpha antithrombin was converted to latent by the glycerol method Source: (natural) Homo sapiens (human) / References: UniProt: P01008 |
-Sugars , 3 types, 6 molecules
#3: Polysaccharide | alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...alpha-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 |
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#4: 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 |
#5: Sugar | ChemComp-NAG / |
-Non-polymers , 2 types, 26 molecules
#6: Chemical | #7: 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: 2.66 Å3/Da / Density % sol: 53.79 % |
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Crystal grow | Temperature: 293 K / pH: 6.7 Details: 12.75% PEG, 50mM K/NaPO4, pH 6.70, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9393 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 29, 2006 |
Radiation | Monochromator: TRANSPARENT DIAMOND WITH SAGITTAL GE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9393 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→51.57 Å / Num. obs: 22751 / % possible obs: 99.2 % / Redundancy: 3.2 % / Biso Wilson estimate: 71.53 Å2 / Rmerge(I) obs: 0.111 / Net I/σ(I): 10.8 |
Reflection shell | Resolution: 2.9→3.06 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.538 / Mean I/σ(I) obs: 2.6 / Rsym value: 0.646 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1E04 Resolution: 2.9→51.57 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Bsol: 53.55 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 52.63 Å2
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Refinement step | Cycle: LAST / Resolution: 2.9→51.57 Å
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Refine LS restraints |
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Xplor file |
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