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Yorodumi- PDB-1tbq: CRYSTAL STRUCTURE OF INSECT DERIVED DOUBLE DOMAIN KAZAL INHIBITOR... -
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-Basic information
Entry | Database: PDB / ID: 1tbq | ||||||
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Title | CRYSTAL STRUCTURE OF INSECT DERIVED DOUBLE DOMAIN KAZAL INHIBITOR RHODNIIN IN COMPLEX WITH THROMBIN | ||||||
Components |
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Keywords | COMPLEX (SERINE PROTEASE/INHIBITOR) / COMPLEX (SERINE PROTEASE-INHIBITOR) / KAZAL-TYPE INHIBITOR / THROMBIN / COMPLEX (SERINE PROTEASE-INHIBITOR) complex | ||||||
Function / homology | Function and homology information fibrinogen binding / thrombin / protein polymerization / positive regulation of blood coagulation / acute-phase response / serine-type endopeptidase inhibitor activity / platelet activation / blood coagulation / collagen-containing extracellular matrix / serine-type endopeptidase activity ...fibrinogen binding / thrombin / protein polymerization / positive regulation of blood coagulation / acute-phase response / serine-type endopeptidase inhibitor activity / platelet activation / blood coagulation / collagen-containing extracellular matrix / serine-type endopeptidase activity / calcium ion binding / proteolysis / extracellular space / extracellular region Similarity search - Function | ||||||
Biological species | Rhodnius prolixus (insect) Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 3.1 Å | ||||||
Authors | Van De Locht, A. / Lamba, D. / Bode, W. | ||||||
Citation | Journal: EMBO J. / Year: 1995 Title: Two heads are better than one: crystal structure of the insect derived double domain Kazal inhibitor rhodniin in complex with thrombin. Authors: van de Locht, A. / Lamba, D. / Bauer, M. / Huber, R. / Friedrich, T. / Kroger, B. / Hoffken, W. / Bode, W. #1: Journal: J.Biol.Chem. / Year: 1993 Title: A Kazal-Type Inhibitor with Thrombin Specificity from Rhodnius Prolixus Authors: Friedrich, T. / Kroger, B. / Bialojan, S. / Lemaire, H.G. / Hoffken, H.W. / Reuschenbach, P. / Otte, M. / Dodt, J. #2: Journal: Protein Sci. / Year: 1992 Title: The Refined 1.9-A X-Ray Crystal Structure of D-Phe-Pro-Arg Chloromethylketone-Inhibited Human Alpha-Thrombin: Structure Analysis, Overall Structure, Electrostatic Properties, Detailed Active- ...Title: The Refined 1.9-A X-Ray Crystal Structure of D-Phe-Pro-Arg Chloromethylketone-Inhibited Human Alpha-Thrombin: Structure Analysis, Overall Structure, Electrostatic Properties, Detailed Active-Site Geometry, and Structure-Function Relationships Authors: Bode, W. / Turk, D. / Karshikov, A. #3: Journal: J.Mol.Biol. / Year: 1991 Title: Refined Structure of the Hirudin-Thrombin Complex Authors: Rydel, T.J. / Tulinsky, A. / Bode, W. / Huber, R. #4: Journal: Embo J. / Year: 1990 Title: Crystal Structure of the Thrombin-Hirudin Complex: A Novel Mode of Serine Protease Inhibition Authors: Grutter, M.G. / Priestle, J.P. / Rahuel, J. / Grossenbacher, H. / Bode, W. / Hofsteenge, J. / Stone, S.R. #5: Journal: Science / Year: 1990 Title: The Structure of a Complex of Recombinant Hirudin and Human Alpha-Thrombin Authors: Rydel, T.J. / Ravichandran, K.G. / Tulinsky, A. / Bode, W. / Huber, R. / Roitsch, C. / Fenton II, J.W. #6: Journal: Embo J. / Year: 1989 Title: The Refined 1.9 A Crystal Structure of Human Alpha-Thrombin: Interaction with D-Phe-Pro-Arg Chloromethylketone and Significance of the Tyr-Pro-Pro-Trp Insertion Segment Authors: Bode, W. / Mayr, I. / Baumann, U. / Huber, R. / Stone, S.R. / Hofsteenge, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1tbq.cif.gz | 173.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1tbq.ent.gz | 144.3 KB | Display | PDB format |
PDBx/mmJSON format | 1tbq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tb/1tbq ftp://data.pdbj.org/pub/pdb/validation_reports/tb/1tbq | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Details | THIS ENTRY CONTAINS TWO THROMBIN MOLECULES AND TWO RHODNIIN MOLECULES. THROMBIN IS CLEAVED BETWEEN RESIDUES 15 AND 16. CHAIN IDENTIFIERS *L* AND *J* ARE USED FOR RESIDUES 1U - 15 OF THROMBIN AND CHAIN IDENTIFIERS *H* AND *K* ARE USED FOR RESIDUES 16 - 247 OF THROMBIN. CHAIN IDENTIFIERS *R* AND *S* ARE USED FOR RHODNIIN. |
-Components
#1: Protein/peptide | Mass: 5735.240 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: PLASMA / References: UniProt: P00735, thrombin #2: Protein | Mass: 29772.422 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: PLASMA / References: UniProt: P00735, thrombin #3: Protein | Mass: 11091.089 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodnius prolixus (insect) / Gene: PRPTI / Organ: PLASMA / Plasmid: PR2C / Gene (production host): PRPTI / Production host: Escherichia coli (E. coli) / References: UniProt: Q06684 #4: Water | ChemComp-HOH / | Sequence details | CHYMOTRYPSINOGEN NUMBERING (RATHER THAN SEQUENTIAL) SYSTEM IS USED, BASED ON THE TOPOLOGICAL ...CHYMOTRYPS | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.06 Å3/Da / Density % sol: 60 % | |||||||||||||||
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Crystal | *PLUS | |||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 6 / Method: vapor diffusion, hanging drop | |||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Wavelength: 1.5418 |
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Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 18, 1993 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→999 Å / Num. obs: 16957 / Observed criterion σ(I): 3 / Redundancy: 1.86 % / Rmerge(I) obs: 0.112 |
Reflection | *PLUS % possible obs: 79.1 % / Num. measured all: 31602 / Rmerge(I) obs: 0.062 |
Reflection shell | *PLUS Highest resolution: 3.1 Å / Lowest resolution: 3.17 Å / % possible obs: 82.3 % |
-Processing
Software |
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Refinement | Resolution: 3.1→8 Å / σ(F): 2 Details: AN OCCUPANCY OF 0.0 SIGNIFIES AN ATOM THAT WAS NOT LOCATED IN THE ELECTRON DENSITY MAPS.
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Displacement parameters | Biso mean: 12.35 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.28 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.1→8 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 12.358 Å2 |