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- PDB-4cpa: REFINED CRYSTAL STRUCTURE OF THE POTATO INHIBITOR COMPLEX OF CARB... -

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Basic information

Entry
Database: PDB / ID: 4cpa
TitleREFINED CRYSTAL STRUCTURE OF THE POTATO INHIBITOR COMPLEX OF CARBOXYPEPTIDASE A AT 2.5 ANGSTROMS RESOLUTION
Components
  • CARBOXYPEPTIDASE A
  • METALLOCARBOXYPEPTIDASE INHIBITOR
KeywordsHYDROLASE (C-TERMINAL PEPTIDASE)
Function / homology
Function and homology information


carboxypeptidase A / leukotriene metabolic process / endopeptidase inhibitor activity / metallocarboxypeptidase activity / proteolysis / extracellular space / zinc ion binding
Similarity search - Function
Carboxypeptidase A inhibitor-like / Carboxypeptidase A inhibitor / Proteinase/amylase inhibitor domain superfamily / 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. / Peptidase family M14 domain profile. ...Carboxypeptidase A inhibitor-like / Carboxypeptidase A inhibitor / Proteinase/amylase inhibitor domain superfamily / 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. / Peptidase family M14 domain profile. / Zn_pept / Peptidase M14, carboxypeptidase A / Zinc carboxypeptidase / Zn peptidases / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GLYCINE / Carboxypeptidase A1 / Metallocarboxypeptidase inhibitor
Similarity search - Component
Biological speciesBos taurus (cattle)
Solanum tuberosum (potato)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsLipscomb, W.N. / Rees, D.C.
Citation
Journal: J.Mol.Biol. / Year: 1982
Title: Refined crystal structure of the potato inhibitor complex of carboxypeptidase A at 2.5 A resolution.
Authors: Rees, D.C. / Lipscomb, W.N.
#1: 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.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1980
Title: Structure of the Potato Inhibitor Complex of Carboxypeptidase a at 2.5-Angstroms Resolution
Authors: Rees, D.C. / Lipscomb, W.N.
#3: Journal: Proc.Natl.Acad.Sci.USA / Year: 1980
Title: Structure of Potato Inhibitor Complex of Carboxypeptidase a at 5.5-Angstroms Resolution
Authors: Rees, D.C. / Lipscomb, W.N.
History
DepositionMar 24, 1982Processing site: BNL
Revision 1.0Jul 29, 1982Provider: repository / Type: Initial release
SupersessionJul 29, 1983ID: 1CPA
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / 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 2.0Sep 27, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Other / Refinement description
Category: atom_site / atom_sites ...atom_site / atom_sites / chem_comp_atom / chem_comp_bond / database_2 / database_PDB_matrix / pdbx_database_remark / pdbx_struct_conn_angle / pdbx_validate_main_chain_plane / pdbx_validate_peptide_omega / pdbx_validate_planes / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / pdbx_validate_torsion / struct_conn / struct_ncs_oper / struct_ref_seq_dif / struct_site
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[1][2] / _atom_sites.fract_transf_matrix[2][1] / _atom_sites.fract_transf_matrix[2][2] / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _database_PDB_matrix.origx[1][1] / _database_PDB_matrix.origx[1][2] / _database_PDB_matrix.origx[2][1] / _database_PDB_matrix.origx[2][2] / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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_auth_asym_id / _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 / _pdbx_validate_main_chain_plane.improper_torsion_angle / _pdbx_validate_peptide_omega.omega / _pdbx_validate_planes.rmsd / _pdbx_validate_rmsd_angle.angle_deviation / _pdbx_validate_rmsd_angle.angle_value / _pdbx_validate_rmsd_bond.bond_deviation / _pdbx_validate_rmsd_bond.bond_value / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_ncs_oper.matrix[1][1] / _struct_ncs_oper.matrix[1][2] / _struct_ncs_oper.matrix[1][3] / _struct_ncs_oper.matrix[2][1] / _struct_ncs_oper.matrix[2][2] / _struct_ncs_oper.matrix[2][3] / _struct_ncs_oper.matrix[3][1] / _struct_ncs_oper.matrix[3][2] / _struct_ncs_oper.vector[1] / _struct_ncs_oper.vector[2] / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Details: Coordinates and associated ncs operations (if present) transformed into standard crystal frame
Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CARBOXYPEPTIDASE A
I: METALLOCARBOXYPEPTIDASE INHIBITOR
B: CARBOXYPEPTIDASE A
J: METALLOCARBOXYPEPTIDASE INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,5338
Polymers77,2524
Non-polymers2814
Water0
1
A: CARBOXYPEPTIDASE A
I: METALLOCARBOXYPEPTIDASE INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7674
Polymers38,6262
Non-polymers1402
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1550 Å2
ΔGint-42 kcal/mol
Surface area13330 Å2
MethodPISA
2
B: CARBOXYPEPTIDASE A
J: METALLOCARBOXYPEPTIDASE INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7674
Polymers38,6262
Non-polymers1402
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1550 Å2
ΔGint-42 kcal/mol
Surface area13320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.450, 53.450, 218.500
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32
Atom site foot note1: SEE REMARK 6.
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.500272, 0.865852, -0.005458), (0.865888, 0.500272, -0.008347), (-0.004438, -0.008913, -0.9995)
Vector: -2.12867, 1.211, -0.334)
DetailsTHERE ARE TWO COPIES OF THE CPA-CPI COMPLEX IN THE ASYMMETRIC UNIT. THE SECOND COPY MAY BE GENERATED FROM THIS ENTRY BY APPLYING THE TRANSFORMATION GIVEN BY THE *MTRIX* RECORDS BELOW.

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Components

#1: Protein CARBOXYPEPTIDASE A /


Mass: 34442.461 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / References: UniProt: P00730, carboxypeptidase A
#2: Protein/peptide METALLOCARBOXYPEPTIDASE INHIBITOR


Mass: 4183.710 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Solanum tuberosum (potato) / References: UniProt: P01075
#3: Chemical ChemComp-GLY / GLYCINE / Glycine


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H5NO2
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 46.93 %
Crystal grow
*PLUS
Method: other
Details: Rees, D.C., (1980) Proc.Natl.Acad.Sci.USA, 77, 4633.

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Data collection

Reflection
*PLUS
Highest resolution: 2.5 Å / Num. all: 23869 / Num. obs: 20550 / % possible obs: 85 % / Num. measured all: 63512 / Rmerge(I) obs: 0.074

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementHighest resolution: 2.5 Å
Refinement stepCycle: LAST / Highest resolution: 2.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5444 0 12 0 5456
Refinement
*PLUS
Rfactor obs: 0.196
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONo_bond_d0.024
X-RAY DIFFRACTIONo_angle_d4.8
X-RAY DIFFRACTIONo_plane_restr0.0360.03
X-RAY DIFFRACTIONo_chiral_restr0.1660.11

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