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- PDB-1hdu: Crystal structure of bovine pancreatic carboxypeptidase A complex... -

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Basic information

Entry
Database: PDB / ID: 1hdu
TitleCrystal structure of bovine pancreatic carboxypeptidase A complexed with aminocarbonylphenylalanine at 1.75 A
ComponentsCARBOXYPEPTIDASE A
KeywordsCARBOXYPEPTIDASE / 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
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 / Peptidase family M14 domain profile. / Peptidase M14, carboxypeptidase A / Zinc carboxypeptidase ...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 / Peptidase family M14 domain profile. / Peptidase M14, carboxypeptidase A / Zinc carboxypeptidase / Zn peptidases / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
D-[(AMINO)CARBONYL]PHENYLALANINE / Carboxypeptidase A1
Similarity search - Component
Biological speciesBOS BOVIS (domestic cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsCho, J.H. / Ha, N.-C. / Chung, S.J. / Kim, D.H. / Choi, K.Y. / Oh, B.-H.
CitationJournal: 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
DepositionNov 17, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 15, 2001Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 9, 2025Group: 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
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_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_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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CARBOXYPEPTIDASE A
B: CARBOXYPEPTIDASE A
D: CARBOXYPEPTIDASE A
E: CARBOXYPEPTIDASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,86412
Polymers137,7704
Non-polymers1,0948
Water10,647591
1
A: CARBOXYPEPTIDASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7163
Polymers34,4421
Non-polymers2742
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: CARBOXYPEPTIDASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7163
Polymers34,4421
Non-polymers2742
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
D: CARBOXYPEPTIDASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7163
Polymers34,4421
Non-polymers2742
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
E: CARBOXYPEPTIDASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7163
Polymers34,4421
Non-polymers2742
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)65.570, 60.524, 74.410
Angle α, β, γ (deg.)90.00, 97.84, 90.00
Int Tables number1
Space group name H-MP1
DetailsBIOLOGICAL_UNIT: MONOMER

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Components

#1: Protein
CARBOXYPEPTIDASE A


Mass: 34442.461 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) BOS BOVIS (domestic cattle) / Organ: PANCREAS / References: UniProt: P00730, carboxypeptidase A
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-ING / D-[(AMINO)CARBONYL]PHENYLALANINE


Mass: 208.214 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H12N2O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 591 / Source method: isolated from a natural source / Formula: H2O
Compound detailsPEPTIDYL-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 PROCARBOXYPEPTIDASE A, CHYMOTRYPSINOGEN C AND PROPROTEINASE E. ALSO KNOWN AS THE ZINC CARBOXYPEPTIDASE FAMILY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.12 Å3/Da / Density % sol: 42.07 %
Crystal growpH: 7.5 / Details: pH 7.50
Crystal grow
*PLUS
Method: microdialysis
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mg/mlprotein11
20.02 MTris-HCl11pH7.5
31.2 M11LiCl
40.14 M12pH7.5LiCl

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Data collection

DiffractionMean temperature: 297 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.75→20 Å / Num. obs: 89359 / % possible obs: 90.4 % / Observed criterion σ(I): 0 / Redundancy: 1.5 % / Rmerge(I) obs: 0.046 / Rsym value: 0.046 / Net I/σ(I): 15
Reflection
*PLUS
Lowest resolution: 20 Å
Reflection shell
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 1.97 Å / % possible obs: 77.4 % / Rmerge(I) obs: 0.149

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Processing

SoftwareName: CNS / Version: 1 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→100 Å / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.229 -5 %RANDOM
Rwork0.198 ---
obs0.198 93239 81.6 %-
Refinement stepCycle: LAST / Resolution: 1.75→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9744 0 64 591 10399
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0054
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.23
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Software
*PLUS
Version: 1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 100 Å / Rfactor obs: 0.187 / Rfactor Rfree: 0.219
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1.235

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