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Yorodumi- PDB-1jvq: Crystal structure at 2.6A of the ternary complex between antithro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1jvq | |||||||||
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Title | Crystal structure at 2.6A of the ternary complex between antithrombin, a P14-P8 reactive loop peptide, and an exogenous tetrapeptide | |||||||||
Components |
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Keywords | HYDROLASE/HYDROLASE INHIBITOR / loop-sheet polymer / beta-barrel / BLOOD CLOTTING / HYDROLASE-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 / 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 | Zhou, A. / Huntington, J.A. / Lomas, D.A. / Carrell, R.W. / Stein, P.E. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 2004 Title: How small peptides block and reverse serpin polymerisation Authors: Zhou, A. / Stein, P.E. / Huntington, J.A. / Sivasothy, P. / Lomas, D.A. / Carrell, R.W. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1jvq.cif.gz | 178.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jvq.ent.gz | 142.4 KB | Display | PDB format |
PDBx/mmJSON format | 1jvq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1jvq_validation.pdf.gz | 500.3 KB | Display | wwPDB validaton report |
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Full document | 1jvq_full_validation.pdf.gz | 537 KB | Display | |
Data in XML | 1jvq_validation.xml.gz | 35.5 KB | Display | |
Data in CIF | 1jvq_validation.cif.gz | 47.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jv/1jvq ftp://data.pdbj.org/pub/pdb/validation_reports/jv/1jvq | HTTPS FTP |
-Related structure data
Related structure data | 1br8S 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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Unit cell |
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-Components
-Protein/peptide , 2 types, 2 molecules CD
#2: Protein/peptide | Mass: 661.660 Da / Num. of mol.: 1 / Fragment: Human antithrombin P14-P8 peptide / Source method: obtained synthetically Details: This sequence occurs naturally in human antithrombin |
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#3: Protein/peptide | Mass: 595.690 Da / Num. of mol.: 1 / Fragment: Cholecystokinin peptide / Source method: obtained synthetically / Details: This sequence occurs naturally in cholecystokinin |
-Protein / Non-polymers , 2 types, 46 molecules LI
#1: Protein | Mass: 49101.016 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: plasma / Source: (natural) Homo sapiens (human) / Tissue: blood / Tissue fraction: plasma / References: UniProt: P01008 #6: Water | ChemComp-HOH / | |
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-Sugars , 2 types, 9 molecules
#4: Sugar | ChemComp-NDG / #5: Sugar | |
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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: 3.08 Å3/Da / Density % sol: 59.8 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: PEG 3350, ammonium fluoride, pH 7.0, VAPOR DIFFUSION, HANGING DROP at 298K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 6.8 / Method: vapor diffusion, hanging 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: PX14.1 / Wavelength: 1.488 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 3, 2001 / Details: mirrors |
Radiation | Monochromator: cooled liquid gallium / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.488 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→40.55 Å / Num. all: 34450 / Num. obs: 34380 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3.7 / Redundancy: 3.7 % / Biso Wilson estimate: 58.3 Å2 / Rmerge(I) obs: 0.103 / Rsym value: 0.088 / Net I/σ(I): 6.5 |
Reflection shell | Resolution: 2.6→2.74 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.648 / Mean I/σ(I) obs: 1.4 / Num. unique all: 4946 / Rsym value: 0.557 / % possible all: 95.1 |
Reflection | *PLUS Lowest resolution: 40.6 Å |
Reflection shell | *PLUS % possible obs: 95.1 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Human antithrombin binary complex, PDB ID 1BR8 Resolution: 2.6→38.63 Å / Rfactor Rfree error: 0.008 / Isotropic thermal model: Restrained / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: flat model / Bsol: 47.6314 Å2 / ksol: 0.331135 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 60.84 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.6→38.63 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.76 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.6 Å / Lowest resolution: 40.6 Å / Rfactor Rwork: 0.205 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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