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Yorodumi- PDB-1qbo: BOVINE TRYPSIN 7-[[6-[[1-(1-IMINOETHYL)PIPERIDIN-4-YL]OXY]-2-METH... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1qbo | ||||||
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Title | BOVINE TRYPSIN 7-[[6-[[1-(1-IMINOETHYL)PIPERIDIN-4-YL]OXY]-2-METHYL-BENZIMIDAZOL-1-YL]METHYL]NAPHTHALENE-2-CARBOXIMIDAMID ZK-806711 INHIBITOR COMPLEX | ||||||
Components | PROTEIN (TRYPSIN) | ||||||
Keywords | HYDROLASE / FACTOR XA / INHIBITOR COMPLEX / SERINE PROTEINASE | ||||||
Function / homology | Function and homology information trypsin / serpin family protein binding / serine protease inhibitor complex / digestion / endopeptidase activity / serine-type endopeptidase activity / proteolysis / extracellular space / metal ion binding Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / DIRECT REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Whitlow, M. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 1999 Title: Crystallographic analysis of potent and selective factor Xa inhibitors complexed to bovine trypsin. Authors: Whitlow, M. / Arnaiz, D.O. / Buckman, B.O. / Davey, D.D. / Griedel, B. / Guilford, W.J. / Koovakkat, S.K. / Liang, A. / Mohan, R. / Phillips, G.B. / Seto, M. / Shaw, K.J. / Xu, W. / Zhao, Z. ...Authors: Whitlow, M. / Arnaiz, D.O. / Buckman, B.O. / Davey, D.D. / Griedel, B. / Guilford, W.J. / Koovakkat, S.K. / Liang, A. / Mohan, R. / Phillips, G.B. / Seto, M. / Shaw, K.J. / Xu, W. / Zhao, Z. / Light, D.R. / Morrissey, M.M. #1: Journal: FEBS Lett. / Year: 1978 Title: Crystal Structure Analysis and Refinement of Two Variants of Trigonal Trypsinogen Authors: Bode, W. / Huber, R. #2: Journal: Acs National Meeting, 1998 A / Year: 1998 Title: Design, synthesis and biological activity of novel factor Xa inhibitors. 9. Benzimidazole-based analogues Authors: Griedel, B.D. / Arnaiz, D. / Sakata, S. / Shaw, K. / Zhao, Z. / Dallas, J. / Koovakkat, S. / Whitlow, M. / Liang, A. / Trinh, L. / Hinchman, J. / Post, J. / Ho, E. / Subramanyam, B. / ...Authors: Griedel, B.D. / Arnaiz, D. / Sakata, S. / Shaw, K. / Zhao, Z. / Dallas, J. / Koovakkat, S. / Whitlow, M. / Liang, A. / Trinh, L. / Hinchman, J. / Post, J. / Ho, E. / Subramanyam, B. / Vergona, R. / Walters, J. / White, K. / Sullivan, M. / Morrissey, M. #3: Journal: FEBS Lett. / Year: 1995 Title: Crystal Structures of Factor Xa Specific Inhibitors in Complex with Trypsin: Structural Grounds for Inhibition of Factor Xa and Selectivity Against Thrombin Authors: Stubbs, M.T. / Huber, R. / Bode, W. #4: Journal: J.Biol.Chem. / Year: 1996 Title: X-ray Structure of Active Site-inhibited Clotting Factor Xa: IMPLICATIONS FOR DRUG DESIGN AND SUBSTRATE RECOGNITION Authors: Brandstetter, H. / Bauer, M. / Huber, R. / Lollar, P. / Bode, W. #5: Journal: Methods (San Diego) / Year: 1990 Title: Analytical and Production Seeding Techniques Authors: Wilson, I.A. / Stura, E.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1qbo.cif.gz | 56.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qbo.ent.gz | 44 KB | Display | PDB format |
PDBx/mmJSON format | 1qbo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qb/1qbo ftp://data.pdbj.org/pub/pdb/validation_reports/qb/1qbo | 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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-Components
#1: Protein | Mass: 23324.287 Da / Num. of mol.: 1 / Fragment: BOVINE TRYPSIN / Source method: isolated from a natural source / Details: BOEHRINGER MANNHEIM CATALOG NUMBER 109,827 / Source: (natural) Bos taurus (cattle) / Organ: PANCREAS / References: UniProt: P00760, trypsin | ||||
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#2: Chemical | #3: Chemical | ChemComp-711 / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.05 Å3/Da / Density % sol: 39.82 % Description: STARTING FROM THE TRYPSIN 2-AMINOBENZIMIDAZOLE STRUCTURE | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: MICROCRYSTALS WERE INITIALLY GROWN USING THE HANGING DROP METHOD IN LINBRO CULTURE PLATES. CRYSTALLIZATION RESERVOIRS CONTAIN 1.8 - 2.0 M AMMONIUM SULFATE, 50 MM TRIS HCL, 10 MM CACL2, PH 7. ...Details: MICROCRYSTALS WERE INITIALLY GROWN USING THE HANGING DROP METHOD IN LINBRO CULTURE PLATES. CRYSTALLIZATION RESERVOIRS CONTAIN 1.8 - 2.0 M AMMONIUM SULFATE, 50 MM TRIS HCL, 10 MM CACL2, PH 7.4. SIX UL OF 15 MG/ML BOVINE TRYPSIN IN 20 MM 2-AMINOBENZIMIDAZOLE WAS ADDED TO 6 UL OF RESERVOIR. MACROSEEDING WAS USED TO GROW LARGE CRYSTALS (REF 5). SINGLE CRYSTALS WERE WASHED IN 0.8 M AMMONIUM SULFATE, 50 MM TRIS HCL, 10 MM CACL2, PH 7.4. THE WASHED CRYSTALS WERE PLACED IN A 18 HOUR OLD HANGING, VAPOR DIFFUSION, HANGING DROP, temperature 297K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 297 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Dec 20, 1994 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→10 Å / Num. all: 17645 / Num. obs: 15600 / % possible obs: 95.4 % / Observed criterion σ(I): 2 / Redundancy: 2.7 % / Rsym value: 0.0976 / Net I/σ(I): 7.6 |
Reflection shell | Resolution: 1.8→2.1 Å / Redundancy: 5.1 % / Rsym value: 0.202 / % possible all: 95 |
Reflection | *PLUS Rmerge(I) obs: 0.098 |
Reflection shell | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 2.1 Å / % possible obs: 95 % / Redundancy: 2 % / Rmerge(I) obs: 0.202 / Mean I/σ(I) obs: 3 |
-Processing
Software |
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Refinement | Method to determine structure: DIRECT REPLACEMENT / Resolution: 1.8→10 Å / σ(F): 2 Stereochemistry target values: W.A.HENDRICKSON (1985) METHODS IN ENZYMOLOGY VOLUME 115, PAGES 370-381.
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Refinement step | Cycle: LAST / Resolution: 1.8→10 Å
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Refine LS restraints |
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Software | *PLUS Name: PROFFT / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS % reflection Rfree: 4 % / Rfactor obs: 0.187 / Rfactor Rwork: 0.187 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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