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- PDB-1o3p: Elaborate Manifold of Short Hydrogen Bond Arrays Mediating Bindin... -
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Basic information
Entry | Database: PDB / ID: 1o3p | ||||||
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Title | Elaborate Manifold of Short Hydrogen Bond Arrays Mediating Binding of Active Site-Directed Serine Protease Inhibitors | ||||||
![]() | (Urokinase-type plasminogen activator) x 2 | ||||||
![]() | BLOOD CLOTTING / hydrolase / serine protease / short hydrogen bond / inhibition mechanism / shift of pKa / trypsin / thrombin / urokinase / factor Xa | ||||||
Function / homology | ![]() u-plasminogen activator / regulation of smooth muscle cell-matrix adhesion / urokinase plasminogen activator signaling pathway / regulation of plasminogen activation / regulation of fibrinolysis / regulation of wound healing / protein complex involved in cell-matrix adhesion / negative regulation of plasminogen activation / regulation of smooth muscle cell migration / regulation of signaling receptor activity ...u-plasminogen activator / regulation of smooth muscle cell-matrix adhesion / urokinase plasminogen activator signaling pathway / regulation of plasminogen activation / regulation of fibrinolysis / regulation of wound healing / protein complex involved in cell-matrix adhesion / negative regulation of plasminogen activation / regulation of smooth muscle cell migration / regulation of signaling receptor activity / serine-type endopeptidase complex / Dissolution of Fibrin Clot / smooth muscle cell migration / plasminogen activation / regulation of cell adhesion mediated by integrin / tertiary granule membrane / negative regulation of fibrinolysis / regulation of cell adhesion / specific granule membrane / serine protease inhibitor complex / fibrinolysis / chemotaxis / blood coagulation / regulation of cell population proliferation / response to hypoxia / positive regulation of cell migration / external side of plasma membrane / serine-type endopeptidase activity / focal adhesion / Neutrophil degranulation / cell surface / signal transduction / proteolysis / extracellular space / extracellular exosome / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Katz, B.A. / Elrod, K. / Verner, E. / Mackman, R.L. / Luong, C. / Shrader, W.D. / Sendzik, M. / Spencer, J.R. / Sprengeler, P.A. / Kolesnikov, A. ...Katz, B.A. / Elrod, K. / Verner, E. / Mackman, R.L. / Luong, C. / Shrader, W.D. / Sendzik, M. / Spencer, J.R. / Sprengeler, P.A. / Kolesnikov, A. / Tai, V.W. / Hui, H.C. / Breitenbucher, J.G. / Allen, D. / Janc, J.W. | ||||||
![]() | ![]() Title: Elaborate manifold of short hydrogen bond arrays mediating binding of active site-directed serine protease inhibitors. Authors: Katz, B.A. / Elrod, K. / Verner, E. / Mackman, R.L. / Luong, C. / Shrader, W.D. / Sendzik, M. / Spencer, J.R. / Sprengeler, P.A. / Kolesnikov, A. / Tai, V.W. / Hui, H.C. / Breitenbucher, J.G. ...Authors: Katz, B.A. / Elrod, K. / Verner, E. / Mackman, R.L. / Luong, C. / Shrader, W.D. / Sendzik, M. / Spencer, J.R. / Sprengeler, P.A. / Kolesnikov, A. / Tai, V.W. / Hui, H.C. / Breitenbucher, J.G. / Allen, D. / Janc, J.W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 136.2 KB | Display | ![]() |
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PDB format | ![]() | 108.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 691.6 KB | Display | ![]() |
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Full document | ![]() | 696.8 KB | Display | |
Data in XML | ![]() | 17.2 KB | Display | |
Data in CIF | ![]() | 25.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1o2gC ![]() 1o2hC ![]() 1o2iC ![]() 1o2jC ![]() 1o2kC ![]() 1o2lC ![]() 1o2mC ![]() 1o2nC ![]() 1o2oC ![]() 1o2pC ![]() 1o2qC ![]() 1o2rC ![]() 1o2sC ![]() 1o2tC ![]() 1o2uC ![]() 1o2vC ![]() 1o2wC ![]() 1o2xC ![]() 1o2yC ![]() 1o2zC ![]() 1o30C ![]() 1o31C ![]() 1o32C ![]() 1o33C ![]() 1o34C ![]() 1o35C ![]() 1o36C ![]() 1o37C ![]() 1o38C ![]() 1o39C ![]() 1o3aC ![]() 1o3bC ![]() 1o3cC ![]() 1o3dC ![]() 1o3eC ![]() 1o3fC ![]() 1o3gC ![]() 1o3hC ![]() 1o3iC ![]() 1o3jC ![]() 1o3kC ![]() 1o3lC ![]() 1o3mC ![]() 1o3nC ![]() 1o3oC C: citing same article ( |
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Similar structure data |
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein/peptide | Mass: 2708.183 Da / Num. of mol.: 1 / Fragment: SHORT CHAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() | ||||
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#2: Protein | Mass: 28435.428 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN / Mutation: N145A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() | ||||
#3: Chemical | #4: Chemical | ChemComp-655 / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 38.5 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 6.5 Details: 2-propanol, PEG 4000, pH 6.5, vapor diffusion at 298 K, pH 6.50 |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 11, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.81→41.66 Å / Num. all: 22960 / Num. obs: 15430 / % possible obs: 67.2 % / Observed criterion σ(I): 0.8 / Redundancy: 2 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 6.1 |
Reflection shell | Resolution: 1.81→1.89 Å / % possible obs: 36.6 % / Rmerge(I) obs: 0.215 / Num. unique all: 2749 |
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Processing
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Refinement | Method to determine structure: ![]() Details: Only Leu_A9 to Lys_A16 are included for the A-chain. Residues prior and after these residues are not visible (disordered). Residues after Lys_B243 are not visible (disordered). Residues ...Details: Only Leu_A9 to Lys_A16 are included for the A-chain. Residues prior and after these residues are not visible (disordered). Residues after Lys_B243 are not visible (disordered). Residues simultaneously refined in two or more conformations are: Lys_A10, Met_B47, Glu_B84, Glu_B86, Leu_B123, Thr_B139, Gln_B192, Arg_B217, Leu_B235. HIS_H57 IS doubly protonated. HIS_H91 and His_H119 are MONOPROTONATED ON the epsilon nitrogen Disordered waters are: HOH382 which is close to conformation 1 of Arg_B217; HOH582 which is close to a symmetry-related equivalent of itself; HOH721 which is close to conformation 1 of Lys_A10; HOH1010 which is close to a symmetry-related equivalent of itself; Some of the waters may correspond to the disordered or mobile termini of the light chain. No energy terms between citrate 1 and 2 are included because they are hydrogen-bonded to one another via an unusually short hydrogen bond between carboxylate / hydroxyl groups. No energy terms are included among HOH_849, and OgSer195, and O6' of the inhibitor. These atoms form a very short multi-centered hydrogen-bonding network.
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Refinement step | Cycle: LAST / Resolution: 1.81→7 Å
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Refine LS restraints |
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