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Yorodumi- PDB-1qb9: BOVINE TRYPSIN 7-[[2-[[1-(1-IMINOETHYL)PIPERIDIN-4-YL]OXY]-9H-CAR... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1qb9 | ||||||
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Title | BOVINE TRYPSIN 7-[[2-[[1-(1-IMINOETHYL)PIPERIDIN-4-YL]OXY]-9H-CARBOZOL-9-YL] METHYL]NAPHTHALENE-2-CARBOXIMIDAMIDE (ZK-806450) COMPLEX | ||||||
Components | PROTEIN (TRYPSIN) | ||||||
Keywords | HYDROLASE / SERINE PROTEINASE / PROTEIN-INHIBITOR COMPLEX / S1 POCKET / FACTOR XA | ||||||
Function / homology | Function and homology information cap snatching / virion component / hydrolase activity / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / nucleotide binding / 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 / Year: 1998 Title: Design, synthesis and biological activity of novel factor Xa inhibitors. 8. Indole-based analogues. Authors: Arnaiz, D.O. / Chou, Y.L. / Mohan, R. / Liang, A / Trinh, L. / Hinchman, J. / Post, J. / Shaw, K. #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. / Kuhne, A. / Bode, W. / Huber, R. / Von Der Saal, W. / Wirthensohn, K. / Engh, R.A. #5: Journal: Methods (San Diego) / Year: 1990 Title: Analytical and Production Seeding Techniques Authors: Stura, E.A. / Wilson, I.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1qb9.cif.gz | 56.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qb9.ent.gz | 43.8 KB | Display | PDB format |
PDBx/mmJSON format | 1qb9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1qb9_validation.pdf.gz | 462.1 KB | Display | wwPDB validaton report |
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Full document | 1qb9_full_validation.pdf.gz | 469.8 KB | Display | |
Data in XML | 1qb9_validation.xml.gz | 7.7 KB | Display | |
Data in CIF | 1qb9_validation.cif.gz | 11.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qb/1qb9 ftp://data.pdbj.org/pub/pdb/validation_reports/qb/1qb9 | HTTPS FTP |
-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 / 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-K / | #4: Chemical | ChemComp-806 / | #5: 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: 38.44 % 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 27, 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: 12238 / Num. obs: 10983 / % possible obs: 67.2 % / Observed criterion σ(I): 2 / Redundancy: 2.83 % / Rsym value: 0.094 / Net I/σ(I): 7.9 |
Reflection shell | Resolution: 1.8→2.1 Å / Redundancy: 2.2 % / Mean I/σ(I) obs: 3.69 / Rsym value: 0.175 / % possible all: 71.4 |
Reflection | *PLUS Rmerge(I) obs: 0.094 |
Reflection shell | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 2.1 Å / % possible obs: 71.4 % / Rmerge(I) obs: 0.175 |
-Processing
Software |
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Refinement | Method to determine structure: DIRECT REPLACEMENT / Resolution: 1.8→10 Å / σ(F): 2 Stereochemistry target values: HENDRICKSON, W.A. (1985) METHODS IN ENZYMOLOGY, VOL. 115, 252-270.
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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 σ(F): 2 / % reflection Rfree: 4 % / Rfactor obs: 0.176 / Rfactor Rwork: 0.176 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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