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Yorodumi- PDB-2hpq: Structures of the noncovalent complexes of human and bovine proth... -
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-Basic information
Entry | Database: PDB / ID: 2hpq | ||||||
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Title | Structures of the noncovalent complexes of human and bovine prothrombin fragment 2 with human ppack-thrombin | ||||||
Components |
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Keywords | HYDROLASE/HYDROLASE INHIBITOR / SERINE PROTEINASE / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | Function and homology information positive regulation of lipid kinase activity / positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / cytolysis by host of symbiont cells / thrombospondin receptor activity / Defective factor XII causes hereditary angioedema / thrombin / neutrophil-mediated killing of gram-negative bacterium / regulation of blood coagulation / ligand-gated ion channel signaling pathway / Defective F8 cleavage by thrombin ...positive regulation of lipid kinase activity / positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / cytolysis by host of symbiont cells / thrombospondin receptor activity / Defective factor XII causes hereditary angioedema / thrombin / neutrophil-mediated killing of gram-negative bacterium / regulation of blood coagulation / ligand-gated ion channel signaling pathway / Defective F8 cleavage by thrombin / Platelet Aggregation (Plug Formation) / negative regulation of platelet activation / negative regulation of astrocyte differentiation / positive regulation of collagen biosynthetic process / negative regulation of cytokine production involved in inflammatory response / positive regulation of blood coagulation / negative regulation of fibrinolysis / Gamma-carboxylation of protein precursors / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / Common Pathway of Fibrin Clot Formation / Removal of aminoterminal propeptides from gamma-carboxylated proteins / fibrinolysis / regulation of cytosolic calcium ion concentration / Intrinsic Pathway of Fibrin Clot Formation / Peptide ligand-binding receptors / positive regulation of release of sequestered calcium ion into cytosol / Regulation of Complement cascade / acute-phase response / Cell surface interactions at the vascular wall / lipopolysaccharide binding / negative regulation of proteolysis / positive regulation of receptor signaling pathway via JAK-STAT / growth factor activity / positive regulation of insulin secretion / platelet activation / response to wounding / Golgi lumen / positive regulation of protein localization to nucleus / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / positive regulation of reactive oxygen species metabolic process / blood coagulation / antimicrobial humoral immune response mediated by antimicrobial peptide / Thrombin signalling through proteinase activated receptors (PARs) / heparin binding / regulation of cell shape / positive regulation of cell growth / G alpha (q) signalling events / collagen-containing extracellular matrix / blood microparticle / cell surface receptor signaling pathway / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of protein phosphorylation / G protein-coupled receptor signaling pathway / endoplasmic reticulum lumen / signaling receptor binding / serine-type endopeptidase activity / calcium ion binding / positive regulation of cell population proliferation / proteolysis / extracellular space / extracellular exosome / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Homo Sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 3.3 Å | ||||||
Authors | Tulinsky, A. / Padmanabhan, K. | ||||||
Citation | Journal: Biochemistry / Year: 1993 Title: Structures of the noncovalent complexes of human and bovine prothrombin fragment 2 with human PPACK-thrombin. Authors: Arni, R.K. / Padmanabhan, K. / Padmanabhan, K.P. / Wu, T.P. / Tulinsky, A. #1: Journal: J.Mol.Biol. / Year: 1991 Title: Structure of the Hirugen and Hirulog 1 Complexes of Alpha-Thrombin Authors: Skrzypczak-Jankun, E. / Carperos, V.E. / Ravichandran, K.G. / Tulinsky, A. / Westbrook, M. / Maraganore, J.M. #2: Journal: Biochemistry / Year: 1991 Title: The Refined Structure of the Epsilon-Aminocaproic Acid Complex of Human Plasminogen Kringle 4 Authors: Wu, T.-P. / Padmanabhan, K. / Tulinsky, A. / Mulichak, A.M. #3: Journal: J.Mol.Biol. / Year: 1991 Title: Structure of Bovine Prothrombin Fragment 1 Refined at 2.25 Angstroms Resolution Authors: Seshadri, T.P. / Tulinsky, A. / Skrzypczak-Jankun, E. / Park, C.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2hpq.cif.gz | 86.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2hpq.ent.gz | 68.8 KB | Display | PDB format |
PDBx/mmJSON format | 2hpq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hp/2hpq ftp://data.pdbj.org/pub/pdb/validation_reports/hp/2hpq | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Atom site foot note | 1: CIS PROLINE - PRO 37 / 2: RESIDUE PHE I 1 IS A D-AMINO ACID. |
-Components
#1: Protein/peptide | Mass: 4096.534 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P00734, thrombin | ||
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#2: Protein | Mass: 29780.219 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P00734, thrombin | ||
#3: Protein | Mass: 8692.646 Da / Num. of mol.: 1 / Fragment: Activation peptide fragment 2 / Source method: isolated from a natural source / Source: (natural) Homo Sapiens (human) / References: UniProt: P00734, thrombin | ||
#4: Chemical | ChemComp-0G7 / | ||
#5: Water | ChemComp-HOH / | ||
Compound details | THROMBIN IS CLEAVED BETWEEN RESIDUES 15 AND 16. CHAIN INDICATOR *L* IS USED FOR RESIDUES 1H - 15 ...THROMBIN IS CLEAVED BETWEEN RESIDUES 15 AND 16. CHAIN INDICATOR *L* IS USED FOR RESIDUES 1H - 15 AND CHAIN INDICATOR *H* IS USED FOR RESIDUES 16 - 247. CHAIN INDICATOR *P* IS USED FOR PROTHROMBI | ||
Nonpolymer details | THE INHIBITOR IS COVALENTLYSequence details | CHYMOTRYPSIN NUMBERING (RATHER THAN SEQUENTIAL) SYSTEM IS USED, BASED ON THE TOPOLOGICAL ALIGNMENT ...CHYMOTRYPS | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 4.49 Å3/Da / Density % sol: 72.6 % | ||||||||||||||||||||
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Crystal | *PLUS Density % sol: 60 % | ||||||||||||||||||||
Crystal grow | *PLUS pH: 5.5 / Method: vapor diffusion, hanging drop / Details: using macroseeding | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 3.2 Å / Num. obs: 9195 / Observed criterion σ(I): 2 / Num. measured all: 51004 / Rmerge(I) obs: 0.065 |
-Processing
Software | Name: PROLSQ / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Rfactor obs: 0.155 / Highest resolution: 3.3 Å Details: A FEW SIDE CHAINS IN BOTH THROMBIN AND FRAGMENT 2 DO NOT HAVE WELL DEFINED ELECTRON DENSITY. THESE ATOMS HAVE BEEN GIVEN OCCUPANCIES OF 0.0 IN THE FILE. THE FOLLOWING RESIDUES IN FRAGMENT 2 ...Details: A FEW SIDE CHAINS IN BOTH THROMBIN AND FRAGMENT 2 DO NOT HAVE WELL DEFINED ELECTRON DENSITY. THESE ATOMS HAVE BEEN GIVEN OCCUPANCIES OF 0.0 IN THE FILE. THE FOLLOWING RESIDUES IN FRAGMENT 2 DO NOT HAVE ELECTRON DENSITY FOR THE SIDE CHAIN BEYOND CB: VAL 302, ARG 305, GLN 307, GLN 310, ARG 312, THR 316, SER 327, LYS 331, SER 341, VAL 343, GLN 344, VAL 346, LYS 367 AND ASN 377. IN ADDITION, THERE WAS NO ELECTRON DENSITY FOR THE 14 N-TERMINAL AND 23 C-TERMINAL INTERKRINGLE PEPTIDES. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 3.3 Å
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Refine LS restraints |
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Software | *PLUS Name: PROLSQ / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 3.3 Å / Lowest resolution: 10 Å / Rfactor obs: 0.155 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 19 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 3.3 Å / Lowest resolution: 3.6 Å / Num. reflection Rfree: 1542 / Rfactor obs: 0.157 |