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Yorodumi- PDB-1pyt: TERNARY COMPLEX OF PROCARBOXYPEPTIDASE A, PROPROTEINASE E, AND CH... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1pyt | ||||||
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Title | TERNARY COMPLEX OF PROCARBOXYPEPTIDASE A, PROPROTEINASE E, AND CHYMOTRYPSINOGEN C | ||||||
Components |
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Keywords | TERNARY COMPLEX (ZYMOGEN) / SERINE PROTEINASE / C-TERMINAL PEPTIDASE | ||||||
Function / homology | Function and homology information Cobalamin (Cbl, vitamin B12) transport and metabolism / chymotrypsin C / carboxypeptidase A / leukotriene metabolic process / digestion / metallocarboxypeptidase activity / serine-type endopeptidase activity / proteolysis / extracellular space / zinc ion binding Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.35 Å | ||||||
Authors | Gomis-Ruth, F.X. / Gomez, M. / Bode, W. / Huber, R. / Aviles, F.X. | ||||||
Citation | Journal: EMBO J. / Year: 1995 Title: The three-dimensional structure of the native ternary complex of bovine pancreatic procarboxypeptidase A with proproteinase E and chymotrypsinogen C. Authors: Gomis-Ruth, F.X. / Gomez, M. / Bode, W. / Huber, R. / Aviles, F.X. #1: Journal: To be Published Title: Procarboxypeptidase A-S6 : Detailed Structure Analysis of the Constituting Subunits and Implications for Their Activation Authors: Gomis-Ruth, F.X. / Gomez, M. / Vendrell, J. / Ventura, S. / Bode, W. / Huber, R. / Aviles, F.X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1pyt.cif.gz | 192.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1pyt.ent.gz | 157.3 KB | Display | PDB format |
PDBx/mmJSON format | 1pyt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1pyt_validation.pdf.gz | 394.2 KB | Display | wwPDB validaton report |
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Full document | 1pyt_full_validation.pdf.gz | 427.7 KB | Display | |
Data in XML | 1pyt_validation.xml.gz | 22.4 KB | Display | |
Data in CIF | 1pyt_validation.cif.gz | 35.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/py/1pyt ftp://data.pdbj.org/pub/pdb/validation_reports/py/1pyt | 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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Unit cell |
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-Components
-PROCARBOXYPEPTIDASE ... , 2 types, 2 molecules AB
#1: Protein | Mass: 10801.105 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: PANCREAS / References: UniProt: P00730, carboxypeptidase A |
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#2: Protein | Mass: 34793.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: PANCREAS / References: UniProt: P00730, carboxypeptidase A |
-Protein , 2 types, 2 molecules CD
#3: Protein | Mass: 27336.564 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: PANCREAS / References: UniProt: P05805 |
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#4: Protein | Mass: 27385.832 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: PANCREAS / References: UniProt: Q7M3E1*PLUS |
-Non-polymers , 3 types, 383 molecules
#5: Chemical | ChemComp-ZN / |
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#6: Chemical | ChemComp-CA / |
#7: Water | ChemComp-HOH / |
-Details
Compound details | THE ACTIVATION PEPTIDE (UP TO ARG 715) OF CTGC IS TWO RESIDUES SHORTER (701-712+715) THAN THE ...THE ACTIVATION |
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Sequence details | FOR RATIONALITY REASONS AND IN ORDER TO PRESERVE THE CHYMOTRYPSINOGEN A (CTGA) NUMBERING FOR BOTH ...FOR RATIONALIT |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.82 Å3/Da / Density % sol: 56.24 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7.1 / Method: vapor diffusion, sitting 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 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→20 Å / Num. obs: 39633 / % possible obs: 87.2 % / Observed criterion σ(I): 3 / Rmerge(I) obs: 0.078 |
-Processing
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Refinement | Resolution: 2.35→6 Å Details: NO PROPER DENSITY WAS OBSERVED FOR SEGMENTS 712 - 716, 846 - 847, AND 888 - 889 OF CTGC. THESE 16 RESIDUES AND SOME SURFACE-LOCATED SIDE-CHAINS (709, 710, 711, 770, 810, 848, 892, 943) HAVE ...Details: NO PROPER DENSITY WAS OBSERVED FOR SEGMENTS 712 - 716, 846 - 847, AND 888 - 889 OF CTGC. THESE 16 RESIDUES AND SOME SURFACE-LOCATED SIDE-CHAINS (709, 710, 711, 770, 810, 848, 892, 943) HAVE BEEN TENTATIVELY TRACED IN ORDER TO PRESERVE CHAIN CONTINUITY AND SET TO ZERO OCCUPANCY (B = 20.0). NO PROPER DENSITY WAS OBSERVED FOR SEGMENT 405 - 409 OF BPE. THIS SEGMENT HAS NOT BEEN TRACED NOR INCLUDED IN THIS MODEL.
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Displacement parameters | Biso mean: 45.4 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.35→6 Å
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Refine LS restraints |
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