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Yorodumi- PDB-1bcs: COMPLEX OF THE WHEAT SERINE CARBOXYPEPTIDASE, CPDW-II, WITH THE M... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1bcs | |||||||||
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Title | COMPLEX OF THE WHEAT SERINE CARBOXYPEPTIDASE, CPDW-II, WITH THE MICROBIAL PEPTIDE ALDEHYDE INHIBITOR, CHYMOSTATIN, AND ARGININE AT 100 DEGREES KELVIN | |||||||||
Components |
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Keywords | HYDROLASE/HYDROLASE INHIBITOR / MICROBIAL PEPTIDE ALDEHYDE INHIBITOR / COMPLEX (SERINE PROTEASE-INHIBITOR) COMPLEX / HYDROLASE-HYDROLASE INHIBITOR COMPLEX | |||||||||
Function / homology | Function and homology information carboxypeptidase D / serine-type carboxypeptidase activity / proteolysis Similarity search - Function | |||||||||
Biological species | Triticum aestivum (bread wheat) Streptomyces hygroscopicus (bacteria) MC521-C8 | |||||||||
Method | X-RAY DIFFRACTION / Resolution: 2.08 Å | |||||||||
Authors | Bullock, T.L. / Remington, S.J. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 1996 Title: Peptide aldehyde complexes with wheat serine carboxypeptidase II: implications for the catalytic mechanism and substrate specificity. Authors: Bullock, T.L. / Breddam, K. / Remington, S.J. #1: Journal: Biochemistry / Year: 1994 Title: Structure of the Complex of L-Benzylsuccinate with Wheat Serine Carboxypeptidase at 2.0 Angstrom Resolution Authors: Bullock, T.L. / Branchaud, B. / Remington, S.J. #2: Journal: Biochemistry / Year: 1992 Title: Refined Atomic Model of Wheat Serine Carboxypeptidase II at 2.2 Angstrom Resolution Authors: Liao, D.I. / Breddam, K. / Sweet, R.M. / Bullock, T. / Remington, S.J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1bcs.cif.gz | 104.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1bcs.ent.gz | 81.4 KB | Display | PDB format |
PDBx/mmJSON format | 1bcs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1bcs_validation.pdf.gz | 585.1 KB | Display | wwPDB validaton report |
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Full document | 1bcs_full_validation.pdf.gz | 610.4 KB | Display | |
Data in XML | 1bcs_validation.xml.gz | 15.1 KB | Display | |
Data in CIF | 1bcs_validation.cif.gz | 23.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bc/1bcs ftp://data.pdbj.org/pub/pdb/validation_reports/bc/1bcs | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Atom site foot note | 1: CIS PROLINE - PRO A 43 / 2: CIS PROLINE - PRO A 54 / 3: CIS PROLINE - PRO A 96 |
-Components
-SERINE CARBOXYPEPTIDASE ... , 2 types, 2 molecules AB
#1: Protein | Mass: 29180.295 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / Tissue: WHEAT GERM / References: UniProt: P08819, carboxypeptidase D |
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#2: Protein | Mass: 17995.229 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / Tissue: WHEAT GERM / References: UniProt: P08819, carboxypeptidase D |
-Protein/peptide , 1 types, 1 molecules C
#3: Protein/peptide | |
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-Sugars , 3 types, 3 molecules
#4: Polysaccharide | alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)]2-acetamido-2-deoxy- ...alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#5: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#7: Sugar | ChemComp-NAG / |
-Non-polymers , 4 types, 387 molecules
#6: Chemical | ChemComp-ARG / |
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#8: Chemical | ChemComp-GOL / |
#9: Chemical | ChemComp-ACT / |
#10: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 4.94 Å3/Da / Density % sol: 75.11 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 4 / Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Wavelength: 1.54 |
Detector | Type: RIGAKU / Detector: IMAGE PLATE |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Redundancy: 2.75 % / Rmerge(I) obs: 0.04 |
Reflection | *PLUS Highest resolution: 2.1 Å / Num. obs: 46630 / % possible obs: 81 % / Num. measured all: 127152 / Rmerge(I) obs: 0.04 |
Reflection shell | *PLUS Highest resolution: 2.1 Å / Lowest resolution: 2.2 Å / % possible obs: 23 % |
-Processing
Software |
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Refinement | Resolution: 2.08→33 Å / σ(F): 0 /
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Refinement step | Cycle: LAST / Resolution: 2.08→33 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.1 Å | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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