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Yorodumi- PDB-4tpi: THE REFINED 2.2-ANGSTROMS (0.22-NM) X-RAY CRYSTAL STRUCTURE OF TH... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4tpi | ||||||
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Title | THE REFINED 2.2-ANGSTROMS (0.22-NM) X-RAY CRYSTAL STRUCTURE OF THE TERNARY COMPLEX FORMED BY BOVINE TRYPSINOGEN, VALINE-VALINE AND THE ARG15 ANALOGUE OF BOVINE PANCREATIC TRYPSIN INHIBITOR | ||||||
Components |
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Keywords | HYDROLASE/HYDROLASE INHIBITOR / COMPLEX (PROTEINASE-INHIBITOR) / HYDROLASE-HYDROLASE INHIBITOR COMPLEX | ||||||
Function / homology | Function and homology information trypsinogen activation / negative regulation of serine-type endopeptidase activity / sulfate binding / potassium channel inhibitor activity / negative regulation of platelet aggregation / zymogen binding / serine protease inhibitor complex / molecular function inhibitor activity / negative regulation of thrombin-activated receptor signaling pathway / cap snatching ...trypsinogen activation / negative regulation of serine-type endopeptidase activity / sulfate binding / potassium channel inhibitor activity / negative regulation of platelet aggregation / zymogen binding / serine protease inhibitor complex / molecular function inhibitor activity / negative regulation of thrombin-activated receptor signaling pathway / cap snatching / virion component / serine-type endopeptidase inhibitor activity / protease binding / hydrolase activity / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / nucleotide binding / calcium ion binding / extracellular space / metal ion binding Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.2 Å | ||||||
Authors | Bode, W. / Walter, J. | ||||||
Citation | Journal: Eur.J.Biochem. / Year: 1984 Title: The refined 2.2-A (0.22-nm) X-ray crystal structure of the ternary complex formed by bovine trypsinogen, valine-valine and the Arg15 analogue of bovine pancreatic trypsin inhibitor Authors: Bode, W. / Walter, J. / Huber, R. / Wenzel, H.R. / Tschesche, H. #1: Journal: J.Mol.Biol. / Year: 1979 Title: The Transition of Bovine Trypsinogen to a Trypsin-Like State Upon Strong Ligand Binding. II. The Binding of the Pancreatic Trypsin Inhibitor and of Isoleucine-Valine and of Sequentially ...Title: The Transition of Bovine Trypsinogen to a Trypsin-Like State Upon Strong Ligand Binding. II. The Binding of the Pancreatic Trypsin Inhibitor and of Isoleucine-Valine and of Sequentially Related Peptides to Trypsinogen and to P-Guanidinobenzoate-Trypsinogen Authors: Bode, W. #2: Journal: J.Mol.Biol. / Year: 1978 Title: The Transition of Bovine Trypsinogen to a Trypsin-Like State Upon Strong Ligand Binding. The Refined Crystal Structures of the Bovine Trypsinogen-Pancreatic Trypsin Inhibitor Complex and of ...Title: The Transition of Bovine Trypsinogen to a Trypsin-Like State Upon Strong Ligand Binding. The Refined Crystal Structures of the Bovine Trypsinogen-Pancreatic Trypsin Inhibitor Complex and of its Ternary Complex with Ile-Val at 1.9 Angstroms Resolution Authors: Bode, W. / Schwager, P. / Huber, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4tpi.cif.gz | 67.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4tpi.ent.gz | 50.1 KB | Display | PDB format |
PDBx/mmJSON format | 4tpi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4tpi_validation.pdf.gz | 408.9 KB | Display | wwPDB validaton report |
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Full document | 4tpi_full_validation.pdf.gz | 413.2 KB | Display | |
Data in XML | 4tpi_validation.xml.gz | 8.2 KB | Display | |
Data in CIF | 4tpi_validation.cif.gz | 12.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tp/4tpi ftp://data.pdbj.org/pub/pdb/validation_reports/tp/4tpi | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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Atom site foot note | 1: SEE REMARK 4. / 2: SEE REMARK 7. / 3: SEE REMARK 8. |
-Components
-Protein , 2 types, 2 molecules ZI
#1: Protein | Mass: 24012.953 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: PANCREAS / References: UniProt: P00760, trypsin |
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#2: Protein | Mass: 6555.582 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source References: UniProt: P00974 |
-Non-polymers , 4 types, 160 molecules
#3: Chemical | #4: Chemical | ChemComp-CA / | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Compound details | RESIDUE SER Z 195 HAS BEEN ALLOWED TO ACCESS INHIBITOR RESIDUES FREELY, I. E. IT IS NOT RESTRICTED ...RESIDUE SER Z 195 HAS BEEN ALLOWED TO ACCESS INHIBITOR RESIDUES FREELY, I. E. IT IS NOT RESTRICTED |
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Nonpolymer details | THE RESIDUES 1016 AND 1017 REPRESENT A DIPEPTIDE (VAL-VAL) BOUND TO THE ENZYME THE 229 AMINO ACIDS ...THE RESIDUES 1016 AND 1017 REPRESENT A DIPEPTIDE (VAL-VAL) BOUND TO THE ENZYME THE 229 AMINO ACIDS OF TRYPSINOGE |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.2 Å3/Da / Density % sol: 61.6 % | ||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 20 ℃ / pH: 6.9 / Method: vapor diffusion | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 2.24 Å / Num. obs: 12422 / % possible obs: 63.8 % / Observed criterion σ(I): 1 / Num. measured all: 18470 / Rmerge(I) obs: 0.069 |
-Processing
Software | Name: EREF / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 2.2→7 Å / Rfactor Rwork: 0.17 Details: THE SIDE CHAIN CONFORMATION OF VAL 1016 AS DESCRIBED IN THE JRNL REFERENCE ABOVE AND AS GIVEN ON THE ATOMS RECORDS BELOW IS ENERGETICALLY UNFAVORABLE. A MORE FAVORABLE CONFORMATION COULD BE ...Details: THE SIDE CHAIN CONFORMATION OF VAL 1016 AS DESCRIBED IN THE JRNL REFERENCE ABOVE AND AS GIVEN ON THE ATOMS RECORDS BELOW IS ENERGETICALLY UNFAVORABLE. A MORE FAVORABLE CONFORMATION COULD BE OBTAINED BY A 180 DEGREE SIDE CHAIN ROTATION ABOUT CHI 1 (VAL 1016 CA - CB). THE SIDE CHAIN CONFORMATION OF VAL S 16 AS DESCRIBED IN THE JRNL REFERENCE ABOVE AND AS GIVEN ON THE ATOMS RECORDS BELOW IS ENERGETICALLY UNFAVORABLE. A MORE FAVORABLE CONFORMATION COULD BE OBTAINED BY A 180 DEGREE SIDE CHAIN ROTATION ABOUT CHI 1 (VAL S 16 CA - CB). | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→7 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 2.24 Å / Rfactor Rwork: 0.17 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |