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- PDB-1o5f: Dissecting and Designing Inhibitor Selectivity Determinants at th... -
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Basic information
Entry | Database: PDB / ID: 1o5f | ||||||
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Title | Dissecting and Designing Inhibitor Selectivity Determinants at the S1 site Using an Artificial Ala190 Protease (Ala190 uPA) | ||||||
![]() | (Serine protease hepsin) x 2 | ||||||
![]() | serine protease / hydrolase / srcr / scavenger receptor cysteine-rich domain / serine protease Ala190 uPA / S1 site / selectivity / conserved water displacement hydrogen bond deficit / trypsin / thrombin / hepsin / factor VIIa | ||||||
Function / homology | ![]() hepsin / pilomotor reflex / Signaling by MST1 / positive regulation of thyroid hormone generation / cochlea morphogenesis / serine-type exopeptidase activity / positive regulation of plasminogen activation / basement membrane disassembly / detection of mechanical stimulus involved in sensory perception of sound / MET Receptor Activation ...hepsin / pilomotor reflex / Signaling by MST1 / positive regulation of thyroid hormone generation / cochlea morphogenesis / serine-type exopeptidase activity / positive regulation of plasminogen activation / basement membrane disassembly / detection of mechanical stimulus involved in sensory perception of sound / MET Receptor Activation / response to thyroid hormone / negative regulation of epithelial to mesenchymal transition / positive regulation by host of viral transcription / positive regulation of hepatocyte proliferation / potassium ion transmembrane transport / serine-type peptidase activity / negative regulation of epithelial cell proliferation / cell-cell junction / peptidase activity / regulation of cell shape / positive regulation of cell growth / apical plasma membrane / serine-type endopeptidase activity / neuronal cell body / positive regulation of gene expression / endoplasmic reticulum membrane / negative regulation of apoptotic process / cell surface / proteolysis / extracellular exosome / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Katz, B.A. / Luong, C. / Ho, J.D. / Somoza, J.R. / Gjerstad, E. / Tang, J. / Williams, S.R. / Verner, E. / Mackman, R.L. / Young, W.B. ...Katz, B.A. / Luong, C. / Ho, J.D. / Somoza, J.R. / Gjerstad, E. / Tang, J. / Williams, S.R. / Verner, E. / Mackman, R.L. / Young, W.B. / Sprengeler, P.A. / Chan, H. / Mortara, K. / Janc, J.W. / McGrath, M.E. | ||||||
![]() | ![]() Title: Dissecting and designing inhibitor selectivity determinants at the S1 site using an artificial Ala190 protease (Ala190 uPA). Authors: Katz, B.A. / Luong, C. / Ho, J.D. / Somoza, J.R. / Gjerstad, E. / Tang, J. / Williams, S.R. / Verner, E. / Mackman, R.L. / Young, W.B. / Sprengeler, P.A. / Chan, H. / Mortara, K. / Janc, J.W. / McGrath, M.E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 161.2 KB | Display | ![]() |
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PDB format | ![]() | 128.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 673.1 KB | Display | ![]() |
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Full document | ![]() | 683.1 KB | Display | |
Data in XML | ![]() | 19.4 KB | Display | |
Data in CIF | ![]() | 28.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1o5aC ![]() 1o5bC ![]() 1o5cC ![]() 1o5dC ![]() 1o5eC ![]() 1o5gC C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 12522.299 Da / Num. of mol.: 1 / Fragment: light chain / Mutation: N67A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() References: UniProt: P05981, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases |
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#2: Protein | Mass: 27573.111 Da / Num. of mol.: 1 / Fragment: heavy chain (catalytic domain) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() References: UniProt: P05981, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases |
#3: Chemical | ChemComp-CR9 / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 42.98 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion / pH: 7.6 Details: 0.2 M ammonium fluoride, 20-25% PEG 3350, 50 mM Tris, pH 7.6, vapor diffusion at 290 K |
-Data collection
Diffraction | Mean temperature: 285 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 29, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.78→25.78 Å / Num. all: 33027 / Num. obs: 29302 / % possible obs: 88.72 % / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 8.9 |
Reflection shell | Resolution: 1.78→1.86 Å / % possible obs: 43.4 % / Rmerge(I) obs: 0.332 / Num. unique all: 4023 |
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Processing
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Refinement | Method to determine structure: ![]() Details: The first four residues of the light chain are not visible and are not included in the model. The loop comprising the sequence "RDPNSEE" between Phe_H97 and Asn_H99 is not visible and is not ...Details: The first four residues of the light chain are not visible and are not included in the model. The loop comprising the sequence "RDPNSEE" between Phe_H97 and Asn_H99 is not visible and is not included in the model. Residues simultaneously refined in two or more conformations are: Ser_L36, Val_L75, Arg_L79, Lys_L112, Leu_H41, Leu_H46, Gln_H73, Ser_H109, Lys_H179, Pro_H185, Thr_H208, Ser_H246. Discretely disordered waters are HOH_212 and HOH_323. His_H40, HIS_H57, and His_H107 are doubly protonated. HIS_H91 is monoprotonated on the epsilon nitrogen No energy terms are included Og_Ser_H195, HOH_383, and O6' and HN3 of the inhibitor. These atoms form a short hydrogen-bonding network.
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Refinement step | Cycle: LAST / Resolution: 1.78→7 Å
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Refine LS restraints |
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