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Yorodumi- PDB-1hdq: Crystal structure of bovine pancreatic carboxypeptidase A complex... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1hdq | ||||||
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Title | Crystal structure of bovine pancreatic carboxypeptidase A complexed with D-N-hydroxyaminocarbonyl phenylalanine at 2.3 A | ||||||
Components | CARBOXYPEPTIDASE A | ||||||
Keywords | CARBOXYPEPTIDASE / CPA / LBHB / INHIBITOR | ||||||
Function / homology | Function and homology information carboxypeptidase A / leukotriene metabolic process / metallocarboxypeptidase activity / proteolysis / extracellular space / zinc ion binding Similarity search - Function | ||||||
Biological species | BOS BOVIS (cattle) | ||||||
Method | X-RAY DIFFRACTION / OTHER / Resolution: 2.3 Å | ||||||
Authors | Cho, J.H. / Ha, N.-C. / Chung, S.J. / Kim, D.H. / Choi, K.Y. / Oh, B.-H. | ||||||
Citation | Journal: Bioorg.Med.Chem. / Year: 2002 Title: Insight Into the Stereochemistry in the Inhibition of Carboxypeptidase a with N-(Hydroxyaminocarbonyl)Phenylalanine: Binding Modes of an Enantiomeric Pair of the Inhibitor to Carboxypeptidase A Authors: Cho, J.H. / Kim, D.H. / Chung, S.J. / Ha, N.-C. / Oh, B.-H. / Choi, K.Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1hdq.cif.gz | 74.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1hdq.ent.gz | 58.5 KB | Display | PDB format |
PDBx/mmJSON format | 1hdq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hd/1hdq ftp://data.pdbj.org/pub/pdb/validation_reports/hd/1hdq | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | BIOLOGICAL_UNIT: MONOMER |
-Components
#1: Protein | Mass: 34517.480 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) BOS BOVIS (cattle) / Organ: PANCREAS / References: UniProt: P00730, carboxypeptidase A |
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#2: Chemical | ChemComp-INF / |
#3: Chemical | ChemComp-ZN / |
#4: Water | ChemComp-HOH / |
Compound details | PEPTIDYL-L-AMINO ACID + H(2)O = PEPTIDE + L-AMINO ACID THE ZYMOGEN IS SECRETED AS A TERNARY COMPLEX ...PEPTIDYL-L-AMINO ACID + H(2)O = PEPTIDE + L-AMINO ACID THE ZYMOGEN IS SECRETED AS A TERNARY COMPLEX COMPOSED OF PROCARBOXY |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 42.95 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.5 / Details: pH 7.50 | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: microdialysis | |||||||||||||||||||||||||||||||||||
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 / Wavelength: 1.5418 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→20 Å / Num. obs: 13199 / % possible obs: 96 % / Observed criterion σ(I): 2 / Redundancy: 2.5 % / Rmerge(I) obs: 0.06 / Rsym value: 0.06 / Net I/σ(I): 33 |
Reflection | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 20 Å / % possible obs: 96 % / Rmerge(I) obs: 0.06 |
Reflection shell | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 2.38 Å / % possible obs: 82.2 % / Rmerge(I) obs: 0.094 |
-Processing
Software | Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: OTHER / Resolution: 2.3→100 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 2.3→100 Å
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Refine LS restraints |
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Software | *PLUS Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 100 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: c_angle_deg / Dev ideal: 1.172 |