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- PDB-3cpa: X-RAY CRYSTALLOGRAPHIC INVESTIGATION OF SUBSTRATE BINDING TO CARB... -

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Basic information

Entry
Database: PDB / ID: 3cpa
TitleX-RAY CRYSTALLOGRAPHIC INVESTIGATION OF SUBSTRATE BINDING TO CARBOXYPEPTIDASE A AT SUBZERO TEMPERATURE
ComponentsCARBOXYPEPTIDASE A
KeywordsHYDROLASE (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
Carboxypeptidase A, carboxypeptidase domain / Carboxypeptidase, activation peptide / Metallocarboxypeptidase-like, propeptide / Carboxypeptidase activation peptide / Zinc carboxypeptidases, zinc-binding region 2 signature. / Zinc carboxypeptidases, zinc-binding region 1 signature. / Zn_pept / Zinc carboxypeptidase / Peptidase family M14 domain profile. / Peptidase M14, carboxypeptidase A ...Carboxypeptidase A, carboxypeptidase domain / Carboxypeptidase, activation peptide / Metallocarboxypeptidase-like, propeptide / Carboxypeptidase activation peptide / Zinc carboxypeptidases, zinc-binding region 2 signature. / Zinc carboxypeptidases, zinc-binding region 1 signature. / Zn_pept / Zinc carboxypeptidase / Peptidase family M14 domain profile. / Peptidase M14, carboxypeptidase A / Zn peptidases / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GLYCINE / TYROSINE / Carboxypeptidase A1
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsLipscomb, 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.
#9: Journal: Atlas of Protein Sequence and Structure (Data Section)
Year: 1972
History
DepositionMar 24, 1982Processing site: BNL
SupersessionJul 29, 1982ID: 1CPA
Revision 1.0Jul 29, 1982Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CARBOXYPEPTIDASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7644
Polymers34,4421
Non-polymers3223
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.600, 60.270, 47.250
Angle α, β, γ (deg.)90.00, 97.27, 90.00
Int Tables number4
Space group name H-MP1211
Atom site foot note1: SEE REMARK 4.

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Components

#1: Protein CARBOXYPEPTIDASE A


Mass: 34442.461 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Tissue: PANCREAS / References: UniProt: P00730, carboxypeptidase A
#2: Chemical ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H5NO2
#3: Chemical ChemComp-TYR / TYROSINE


Type: L-peptide linking / Mass: 181.189 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H11NO3
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
Has protein modificationY
Nonpolymer detailsRESIDUES 501 AND 502 FORM THE DIPEPTIDE SUBSTRATE (GLY-TYR) BOUND TO THE ENZYME

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 41.45 %
Crystal growDetails: 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
IDConc.Common nameCrystal-IDSol-IDChemical formula
11.2 M11LiCl
20.02 MTris-HCl11
30.2 M12LiCl
40.02 MTris-HCl12

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementHighest resolution: 2 Å
Refinement stepCycle: LAST / Highest resolution: 2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2437 0 18 0 2455
Refinement
*PLUS
Highest resolution: 2 Å / Rfactor obs: 0.162
Solvent computation
*PLUS
Displacement parameters
*PLUS

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