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Yorodumi- PDB-3cpa: X-RAY CRYSTALLOGRAPHIC INVESTIGATION OF SUBSTRATE BINDING TO CARB... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3cpa | |||||||||
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Title | X-RAY CRYSTALLOGRAPHIC INVESTIGATION OF SUBSTRATE BINDING TO CARBOXYPEPTIDASE A AT SUBZERO TEMPERATURE | |||||||||
Components | CARBOXYPEPTIDASE A | |||||||||
Keywords | HYDROLASE (C-TERMINAL PEPTIDASE) | |||||||||
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 taurus (cattle) | |||||||||
Method | X-RAY DIFFRACTION / Resolution: 2 Å | |||||||||
Authors | Lipscomb, W.N. | |||||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 1986 Title: X-ray crystallographic investigation of substrate binding to carboxypeptidase A at subzero temperature. Authors: Christianson, D.W. / Lipscomb, W.N. #1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1983 Title: Crystallographic Studies on Apocarboxypeptidase a and the Complex with Glycyl-L-Tyrosine Authors: Rees, D.C. / Lipscomb, W.N. #2: Journal: J.Mol.Biol. / Year: 1983 Title: Refined Crystal Structure of Carboxypeptidase a at 1.54 Angstroms Resolution. Authors: Rees, D.C. / Lewis, M. / Lipscomb, W.N. #3: Journal: Proc.Natl.Acad.Sci.USA / Year: 1981 Title: Binding of Ligands to the Active Site of Carboxypeptidase A Authors: Rees, D.C. / Lipscomb, W.N. #4: Journal: Proc.Natl.Acad.Sci.USA / Year: 1981 Title: Zinc Environment and Cis Peptide Bonds in Carboxypeptidase a at 1.75-Angstroms Resolution Authors: Rees, D.C. / Lewis, M. / Honzatko, R.B. / Lipscomb, W.N. / Hardman, K.D. #5: Journal: Proc.Natl.Acad.Sci.USA / Year: 1980 Title: Carboxypeptidase a Mechanisms Authors: Lipscomb, W.N. #6: Journal: Adv.Protein Chem. / Year: 1971 Title: Carboxypeptidase A,A Protein and an Enzyme Authors: Quiocho, F.A. / Lipscomb, W.N. #7: Journal: Acc.Chem.Res. / Year: 1970 Title: Structure and Mechanism in the Enzymatic Activity of Carboxypeptidase a and Relations to Chemical Sequence Authors: Lipscomb, W.N. #8: Journal: Brookhaven Symposia in Biology / Year: 1969 Title: The Structure of Carboxypeptidase A, Vii.The 2.0-Angstroms Resolution Studies of the Enzyme and of its Complex with Glycyltyrosine,and Mechanistic Deductions Authors: Lipscomb, W.N. / Hartsuck, J.A. / Reekejunior, G.N. / Quiocho, F.A. / Bethge, P.H. / Ludwig, M.L. / Steitz, T.A. / Muirhead, H. / Coppola, J.C. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3cpa.cif.gz | 62.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3cpa.ent.gz | 48.5 KB | Display | PDB format |
PDBx/mmJSON format | 3cpa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3cpa_validation.pdf.gz | 396.5 KB | Display | wwPDB validaton report |
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Full document | 3cpa_full_validation.pdf.gz | 412.4 KB | Display | |
Data in XML | 3cpa_validation.xml.gz | 10.3 KB | Display | |
Data in CIF | 3cpa_validation.cif.gz | 14.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cp/3cpa ftp://data.pdbj.org/pub/pdb/validation_reports/cp/3cpa | 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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Atom site foot note | 1: SEE REMARK 4. |
-Components
#1: Protein | Mass: 34442.461 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Tissue: PANCREAS / References: UniProt: P00730, carboxypeptidase A |
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#2: Chemical | ChemComp-GLY / |
#3: Chemical | ChemComp-TYR / |
#4: Chemical | ChemComp-ZN / |
Nonpolymer details | RESIDUES 501 AND 502 FORM THE DIPEPTIDE SUBSTRATE (GLY-TYR) BOUND TO THE ENZYME |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.45 % | ||||||||||||||||||||||||||||||
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Crystal grow | Details: THE COMPLEX WAS PREPARED BY DIFFUSION OF GLY-TYR INTO CPA CRYSTALS. THE OCCUPANCY OF THE GLY-TYR IS APPROXIMATELY FORTY PERCENT. | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7.4 / Method: microdialysis | ||||||||||||||||||||||||||||||
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 |
-Processing
Software | Name: PROLSQ / Classification: refinement | ||||||||||||
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Refinement | Highest resolution: 2 Å | ||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 2 Å
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Refinement | *PLUS Highest resolution: 2 Å / Rfactor obs: 0.162 | ||||||||||||
Solvent computation | *PLUS | ||||||||||||
Displacement parameters | *PLUS |