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- PDB-5cpa: REFINED CRYSTAL STRUCTURE OF CARBOXYPEPTIDASE A AT 1.54 ANGSTROMS... -

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Entry
Database: PDB / ID: 5cpa
TitleREFINED CRYSTAL STRUCTURE OF CARBOXYPEPTIDASE A AT 1.54 ANGSTROMS RESOLUTION.
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
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / Resolution: 1.54 Å
AuthorsLipscomb, W.N.
Citation
Journal: J.Mol.Biol. / Year: 1983
Title: Refined crystal structure of carboxypeptidase A at 1.54 A resolution.
Authors: Rees, D.C. / Lewis, M. / 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: 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.
#3: 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.
#4: Journal: Proc.Natl.Acad.Sci.USA / Year: 1980
Title: Carboxypeptidase a Mechanisms
Authors: Lipscomb, W.N.
#5: Journal: Adv.Protein Chem. / Year: 1971
Title: Carboxypeptidase A,A Protein and an Enzyme
Authors: Quiocho, F.A. / Lipscomb, W.N.
#6: 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.
#7: 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.
#8: Journal: Atlas of Protein Sequence and Structure (Data Section)
Year: 1972
History
DepositionMay 6, 1982Processing site: BNL
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 30, 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_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_struct_conn_angle.ptnr1_PDB_ins_code / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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_PDB_ins_code / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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.pdbx_dist_value / _struct_conn.pdbx_ptnr2_PDB_ins_code / _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_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)34,5082
Polymers34,4421
Non-polymers651
Water5,675315
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.
2: SEE REMARK 7. COORDINATES FOR THIS ATOM WERE SYMMETRY GENERATED USING THE OPERATION, (XB,YB,ZB) = (-XA,YA+30.135,-ZA) (XB,YB,ZB) ARE THE COORDINATES OF ATOMS WITH INSERT CODE *B*. (XA,YA,ZA) ARE ...2: SEE REMARK 7. COORDINATES FOR THIS ATOM WERE SYMMETRY GENERATED USING THE OPERATION, (XB,YB,ZB) = (-XA,YA+30.135,-ZA) (XB,YB,ZB) ARE THE COORDINATES OF ATOMS WITH INSERT CODE *B*. (XA,YA,ZA) ARE THE COORDINATES OF ATOMS WITH INSERT CODE *A*.
3: SEE REMARK 7. COORDINATES FOR THIS ATOM WERE SYMMETRY GENERATED USING THE OPERATION, (XC,YC,ZC) = (-XA+5.979,YA+30.135,-ZA-46.870) (XC,YC,ZC) ARE THE COORDINATES OF ATOMS WITH INSERT CODE *C*. ...3: SEE REMARK 7. COORDINATES FOR THIS ATOM WERE SYMMETRY GENERATED USING THE OPERATION, (XC,YC,ZC) = (-XA+5.979,YA+30.135,-ZA-46.870) (XC,YC,ZC) ARE THE COORDINATES OF ATOMS WITH INSERT CODE *C*. (XA,YA,ZA) ARE THE COORDINATES OF ATOMS WITH INSERT CODE *A*.
4: SEE REMARK 7. COORDINATES FOR THIS ATOM WERE SYMMETRY GENERATED USING THE OPERATION, (XD,YD,ZD) = (-XA,YA-30.135,-ZA) (XD,YD,ZD) ARE THE COORDINATES OF ATOMS WITH INSERT CODE *D*. (XA,YA,ZA) ARE ...4: SEE REMARK 7. COORDINATES FOR THIS ATOM WERE SYMMETRY GENERATED USING THE OPERATION, (XD,YD,ZD) = (-XA,YA-30.135,-ZA) (XD,YD,ZD) ARE THE COORDINATES OF ATOMS WITH INSERT CODE *D*. (XA,YA,ZA) ARE THE COORDINATES OF ATOMS WITH INSERT CODE *A*.
5: SEE REMARK 7. COORDINATES FOR THIS ATOM WERE SYMMETRY GENERATED USING THE OPERATION, (XE,YE,ZE) = (XA+51.61,YA,ZA) (XE,YE,ZE) ARE THE COORDINATES OF ATOMS WITH INSERT CODE *E*. (XA,YA,ZA) ARE THE ...5: SEE REMARK 7. COORDINATES FOR THIS ATOM WERE SYMMETRY GENERATED USING THE OPERATION, (XE,YE,ZE) = (XA+51.61,YA,ZA) (XE,YE,ZE) ARE THE COORDINATES OF ATOMS WITH INSERT CODE *E*. (XA,YA,ZA) ARE THE COORDINATES OF ATOMS WITH INSERT CODE *A*.
6: SEE REMARK 7. COORDINATES FOR THIS ATOM WERE SYMMETRY GENERATED USING THE OPERATION, (XF,YF,ZF) = (-XA-51.61,YA+30.135,-ZA) (XF,YF,ZF) ARE THE COORDINATES OF ATOMS WITH INSERT CODE *F*. (XA,YA,ZA) ...6: SEE REMARK 7. COORDINATES FOR THIS ATOM WERE SYMMETRY GENERATED USING THE OPERATION, (XF,YF,ZF) = (-XA-51.61,YA+30.135,-ZA) (XF,YF,ZF) ARE THE COORDINATES OF ATOMS WITH INSERT CODE *F*. (XA,YA,ZA) ARE THE COORDINATES OF ATOMS WITH INSERT CODE *A*.
7: SEE REMARK 7. COORDINATES FOR THIS ATOM WERE SYMMETRY GENERATED USING THE OPERATION, (XG,YG,ZG) = (XA-5.979,YA,ZA+46.870) (XG,YG,ZG) ARE THE COORDINATES OF ATOMS WITH INSERT CODE *G*. (XA,YA,ZA) ...7: SEE REMARK 7. COORDINATES FOR THIS ATOM WERE SYMMETRY GENERATED USING THE OPERATION, (XG,YG,ZG) = (XA-5.979,YA,ZA+46.870) (XG,YG,ZG) ARE THE COORDINATES OF ATOMS WITH INSERT CODE *G*. (XA,YA,ZA) ARE THE COORDINATES OF ATOMS WITH INSERT CODE *A*.
8: SEE REMARK 7. COORDINATES FOR THIS ATOM WERE SYMMETRY GENERATED USING THE OPERATION, (XH,YH,ZH) = (-XA-51.61,YA-30.135,-ZA) (XH,YH,ZH) ARE THE COORDINATES OF ATOMS WITH INSERT CODE *H*. (XA,YA,ZA) ...8: SEE REMARK 7. COORDINATES FOR THIS ATOM WERE SYMMETRY GENERATED USING THE OPERATION, (XH,YH,ZH) = (-XA-51.61,YA-30.135,-ZA) (XH,YH,ZH) ARE THE COORDINATES OF ATOMS WITH INSERT CODE *H*. (XA,YA,ZA) ARE THE COORDINATES OF ATOMS WITH INSERT CODE *A*.
9: SEE REMARK 7. COORDINATES FOR THIS ATOM WERE SYMMETRY GENERATED USING THE OPERATION, (XI,YI,ZI) = (-XA-45.631,YA+30.135,-ZA-46.870) (XI,YI,ZI) ARE THE COORDINATES OF ATOMS WITH INSERT CODE *I*. ...9: SEE REMARK 7. COORDINATES FOR THIS ATOM WERE SYMMETRY GENERATED USING THE OPERATION, (XI,YI,ZI) = (-XA-45.631,YA+30.135,-ZA-46.870) (XI,YI,ZI) ARE THE COORDINATES OF ATOMS WITH INSERT CODE *I*. (XA,YA,ZA) ARE THE COORDINATES OF ATOMS WITH INSERT CODE *A*.
10: SEE REMARK 7. COORDINATES FOR THIS ATOM WERE SYMMETRY GENERATED USING THE OPERATION, (XJ,YJ,ZJ) = (-XA-45.631,YA-30.135,-ZA-46.870) (XJ,YJ,ZJ) ARE THE COORDINATES OF ATOMS WITH INSERT CODE *J*. ...10: SEE REMARK 7. COORDINATES FOR THIS ATOM WERE SYMMETRY GENERATED USING THE OPERATION, (XJ,YJ,ZJ) = (-XA-45.631,YA-30.135,-ZA-46.870) (XJ,YJ,ZJ) ARE THE COORDINATES OF ATOMS WITH INSERT CODE *J*. (XA,YA,ZA) ARE THE COORDINATES OF ATOMS WITH INSERT CODE *A*.
11: SEE REMARK 7. COORDINATES FOR THIS ATOM WERE SYMMETRY GENERATED USING THE OPERATION, (XK,YK,ZK) = (XA-51.61,YA,ZA) (XK,YK,ZK) ARE THE COORDINATES OF ATOMS WITH INSERT CODE *K*. (XA,YA,ZA) ARE THE ...11: SEE REMARK 7. COORDINATES FOR THIS ATOM WERE SYMMETRY GENERATED USING THE OPERATION, (XK,YK,ZK) = (XA-51.61,YA,ZA) (XK,YK,ZK) ARE THE COORDINATES OF ATOMS WITH INSERT CODE *K*. (XA,YA,ZA) ARE THE COORDINATES OF ATOMS WITH INSERT CODE *A*.
12: SEE REMARK 7. COORDINATES FOR THIS ATOM WERE SYMMETRY GENERATED USING THE OPERATION, (XL,YL,ZL) = (XA+5.979,YA,ZA-46.870) (XL,YL,ZL) ARE THE COORDINATES OF ATOMS WITH INSERT CODE *L*. (XA,YA,ZA) ...12: SEE REMARK 7. COORDINATES FOR THIS ATOM WERE SYMMETRY GENERATED USING THE OPERATION, (XL,YL,ZL) = (XA+5.979,YA,ZA-46.870) (XL,YL,ZL) ARE THE COORDINATES OF ATOMS WITH INSERT CODE *L*. (XA,YA,ZA) ARE THE COORDINATES OF ATOMS WITH INSERT CODE *A*.

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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) / References: UniProt: P00730, carboxypeptidase A
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 315 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.12 Å3/Da / Density % sol: 41.85 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.5 / Method: microdialysis
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.2 M11LiCl
220 mMTris-HCl11

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Data collection

Reflection
*PLUS
Highest resolution: 1.54 Å / Num. obs: 32080

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementHighest resolution: 1.54 Å
Refinement stepCycle: LAST / Highest resolution: 1.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2437 0 1 315 2753
Refinement
*PLUS
Rfactor all: 0.19
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONo_bond_d0.025
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_deg3.6
X-RAY DIFFRACTIONo_plane_restr0.0380.055
X-RAY DIFFRACTIONo_chiral_restr0.2630.15

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