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Yorodumi- PDB-1br8: IMPLICATIONS FOR FUNCTION AND THERAPY OF A 2.9A STRUCTURE OF BINA... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1br8 | ||||||
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Title | IMPLICATIONS FOR FUNCTION AND THERAPY OF A 2.9A STRUCTURE OF BINARY-COMPLEXED ANTITHROMBIN | ||||||
Components |
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Keywords | BLOOD CLOTTING / SERPINS / ANTITHROMBIN / BINARY-COMPLEX / HEPARIN / POLYMERISATION / THROMBOSIS / EMPHYSEMA / CIRRHOSIS | ||||||
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 | Skinner, R. / Chang, W.S.W. / Jin, L. / Pei, X.Y. / Huntington, J.A. / Abrahams, J.P. / Carrell, R.W. / Lomas, D.A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1998 Title: Implications for function and therapy of a 2.9 A structure of binary-complexed antithrombin. Authors: Skinner, R. / Chang, W.S. / Jin, L. / Pei, X. / Huntington, J.A. / Abrahams, J.P. / Carrell, R.W. / Lomas, D.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1br8.cif.gz | 170.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1br8.ent.gz | 135.9 KB | Display | PDB format |
PDBx/mmJSON format | 1br8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/br/1br8 ftp://data.pdbj.org/pub/pdb/validation_reports/br/1br8 | HTTPS FTP |
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-Related structure data
Related structure data | 2antS 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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3 |
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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 / Source: (natural) Homo sapiens (human) / Strain: 1Q23-25 / Tissue: PLASMA / References: UniProt: P01008 #2: Protein/peptide | | Mass: 1089.197 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: PEPTIDE WAS CHEMICALLY SYNTHESIZED. #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: 2.6 Å3/Da / Density % sol: 45 % / Description: DATA WERE COLLECTED USING OSCILLATION METHOD | |||||||||||||||||||||||||
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Crystal grow | pH: 6.9 Details: 30.6% W/V PEG4000, 35% V/V GLYCEROL, 30 MM CACODYLATE, PH 6.9 | |||||||||||||||||||||||||
Crystal | *PLUS | |||||||||||||||||||||||||
Crystal grow | *PLUS Method: batch method | |||||||||||||||||||||||||
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 | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 15, 1997 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.488 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→20 Å / Num. obs: 23603 / % possible obs: 95.4 % / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Biso Wilson estimate: 35.934 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 13.6 |
Reflection shell | Resolution: 2.94→3.12 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.13 / Mean I/σ(I) obs: 5.6 / % possible all: 87.8 |
Reflection shell | *PLUS % possible obs: 87.8 % / Rmerge(I) obs: 0.13 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2ANT Resolution: 2.9→6 Å / Isotropic thermal model: TNT BCORREL V1.0 / σ(F): 0 / Stereochemistry target values: TNT PROTGEO
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Refinement step | Cycle: LAST / Resolution: 2.9→6 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Version: 5 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.9 Å / Lowest resolution: 6 Å / σ(F): 0 / Num. reflection Rfree: 898 / % reflection Rfree: 4.2 % / Rfactor all: 0.23 / Rfactor obs: 0.228 / Rfactor Rfree: 0.297 / Rfactor Rwork: 0.228 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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