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Yorodumi- PDB-2hpp: Structures of the noncovalent complexes of human and bovine proth... -
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-Basic information
Entry | Database: PDB / ID: 2hpp | ||||||
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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 / HYDROLASE-HYDROLASE INHIBITOR COMPLEX / SERINE PROTEINASE | ||||||
Function / homology | Function and homology information fibrinogen binding / 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 ...fibrinogen binding / 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 / protein polymerization / 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) Bos Taurus (cattle) | ||||||
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 | 2hpp.cif.gz | 85.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2hpp.ent.gz | 68.8 KB | Display | PDB format |
PDBx/mmJSON format | 2hpp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hp/2hpp ftp://data.pdbj.org/pub/pdb/validation_reports/hp/2hpp | 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 / Fragment: UNP residues 328-363 / 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 / Fragment: UNP residues 364-622 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P00734, thrombin |
#3: Protein | Mass: 8836.645 Da / Num. of mol.: 1 / Fragment: UNP residues 214-292 / Source method: isolated from a natural source / Source: (natural) Bos Taurus (cattle) / References: UniProt: P00735, thrombin |
#4: Chemical | ChemComp-0G7 / |
#5: Water | ChemComp-HOH / |
Nonpolymer details | THE UNBOUND FORM OF THE INHIBITOR IS D-PHE-PRO-ARG-CHLOROMETHYLKETONE. UPON REACTION WITH PROTEIN ...THE UNBOUND FORM OF THE INHIBITOR IS D-PHE-PRO-ARG-CHLOROMETH |
Sequence details | CHYMOTRYPSIN NUMBERING SYSTEM IS USED, BASED ON THE TOPOLOGICAL ALIGNMENT WITH THE STRUCTURE OF ...CHYMOTRYPS |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 4.52 Å3/Da / Density % sol: 72.8 % | ||||||||||||||||||||
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Crystal | *PLUS Density % sol: 60 % | ||||||||||||||||||||
Crystal grow | *PLUS pH: 6.5 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||
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: 3.3 Å / Num. obs: 9115 / % possible obs: 70 % / Observed criterion σ(I): 2 / Num. measured all: 62904 / Rmerge(I) obs: 0.052 |
-Processing
Software | Name: PROLSQ / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Rfactor obs: 0.157 / 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 FOR THE FOLLOWING: ARG 310, ARG 312, ...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 FOR THE FOLLOWING: ARG 310, ARG 312, THR 316, ARG 321, SER 327, GLU 328, VAL 343, AND ASN 377. IN ADDITION THERE WAS NO ELECTRON DENSITY FOR THE 14 N-TERMINAL AND 25 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 / Num. reflection obs: 9115 / σ(F): 2 / Rfactor obs: 0.157 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 21 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: 3.6 / Num. reflection Rwork: 1208 / Num. reflection obs: 3.3 / Rfactor obs: 0.154 |