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1yme

STRUCTURE OF CARBOXYPEPTIDASE

Method: X-RAY DIFFRACTION Dmax: 63.8 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

CARBOXYPEPTIDASE A ALPHA

OrganismNot specified

UniProt P00730

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 111–419 Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 1.53 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 1YME Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1ARL CARBOXYPEPTIDASE A WITH ZN REMOVED Deposited 1994-11-22 Different construct Different ligand/ion Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 111–417（307 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.88 Å
1ARM CARBOXYPEPTIDASE A WITH ZN REPLACED BY HG Deposited 1994-11-22 Different ligand/ion Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 111–419（309 aa）
Not recorded HG MERCURY (II) ION × 4 CU COPPER (II) ION × 1 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.76 Å
1BAV CARBOXYPEPTIDASE A COMPLEXED WITH 2-BENZYL-3-IODO-PROPANOIC ACID (BIP) Deposited 1996-11-14 Different ligand/ion Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 111–419（309 aa）
Not recorded ZN ZINC ION × 1 BIP 2-BENZYL-3-IODOPROPANOIC ACID × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.60 Å R-free 0.213
1BAV CARBOXYPEPTIDASE A COMPLEXED WITH 2-BENZYL-3-IODO-PROPANOIC ACID (BIP) Deposited 1996-11-14 Different ligand/ion Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 111–419（309 aa）
Not recorded ZN ZINC ION × 1 BIP 2-BENZYL-3-IODOPROPANOIC ACID × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.60 Å R-free 0.213
1BAV CARBOXYPEPTIDASE A COMPLEXED WITH 2-BENZYL-3-IODO-PROPANOIC ACID (BIP) Deposited 1996-11-14 Different ligand/ion Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 111–419（309 aa）
Not recorded ZN ZINC ION × 1 BIP 2-BENZYL-3-IODOPROPANOIC ACID × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.60 Å R-free 0.213
1BAV CARBOXYPEPTIDASE A COMPLEXED WITH 2-BENZYL-3-IODO-PROPANOIC ACID (BIP) Deposited 1996-11-14 Different ligand/ion Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 111–419（309 aa）
Not recorded ZN ZINC ION × 1 BIP 2-BENZYL-3-IODOPROPANOIC ACID × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.60 Å R-free 0.213
1CBX CRYSTAL STRUCTURE OF THE COMPLEX BETWEEN CARBOXYPEPTIDASE A AND THE BIPRODUCT ANALOG INHIBITOR L-BENZYLSUCCINATE AT 2.0 ANGSTROMS RESOLUTION Deposited 1991-10-31 Different construct Different ligand/ion Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 111–417（307 aa）
Not recorded ZN ZINC ION × 1 BZS L-BENZYLSUCCINIC ACID × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.00 Å
1CPS STRUCTURAL COMPARISON OF SULFODIIMINE AND SULFONAMIDE INHIBITORS IN THEIR COMPLEXES WITH ZINC ENZYMES Deposited 1992-02-18 Different construct Different ligand/ion Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 111–417（307 aa）
Not recorded ZN ZINC ION × 1 CPM S-(2-CARBOXY-3-PHENYLPROPYL)THIODIIMINE-S-METHANE × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.25 Å
1CPX BETA FORM OF CARBOXYPEPTIDASE A (RESIDUES 3-307) FROM BOVINE PANCREAS IN AN ORTHORHOMBIC CRYSTAL FORM WITH TWO ZINC IONS IN THE ACTIVE SITE. Deposited 1998-07-27 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 111–417（307 aa）
Not recorded ZN ZINC ION × 2 OH HYDROXIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions MICRODIALYSIS；pH 7.5；CPA FROM SIGMA #C0261 WAS DISSOLVED IN 1.0 M LICL WITH 20 MM TRIS-HCL PH 7.5 TO GIVE 12 MG/ML AND USED WITHOUT FURTHER PURIFICATION. THIS PROTEIN SOLUTION WAS PLACED IN 50 MICROL DIALYSIS BUTTONS FROM HAMPTON RESEARCH AND DIALYZED AGAINST A 2 ML RESERVOIR OF THE ABOVE MENTIONED BUFFER WHILE LOWERING THE EXTERNAL LICL CONCENTRATION BY 25% EVERY OTHER DAY. THE CRYSTALS APPEARED A~0.24 M LICL AND WAS STORED AT 0.30M LICL. IF THIS PROCEDURE DOES NOT WORK BY ITSELF AND YOU END UP WITH THE MONOCLINIC ALPHA-FORM (1-307), YOU CAN TRY TO AD TRACES OF TRYPSIN (~10 MICROG/ML) TO THE PROTEIN SOLUTION TO PROVOKE FORMATION OF THE BETA-FORM (3-307), micro dialysis
Resolution 2.00 Å R-free 0.226
1EE3 Cadmium-substituted bovine pancreatic carboxypeptidase A (alfa-form) at pH 7.5 and 2 mM chloride in monoclinic crystal form Deposited 2000-01-30 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain P 111–419（309 aa）
Not recorded CD CADMIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions MICRODIALYSIS；pH 7.5；293 K；Lithium Chloride, Tris-HNO3, Cadmium Chloride, pH 7.5, MICRODIALYSIS, temperature 293K
Resolution 1.70 Å R-free 0.198
1ELL CADMIUM-SUBSTITUTED BOVINE PANCREATIC CARBOXYPEPTIDASE A (ALFA-FORM) AT PH 7.5 AND 0.25 M CHLORIDE IN MONOCLINIC CRYSTAL FORM. Deposited 2000-03-14 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain P 111–419（309 aa） Fragment：ALFA-FORM
Not recorded CD CADMIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions MICRODIALYSIS；pH 7.5；293 K；Lithium Chloride, Tris-HNO3, Cadmium Chloride, pH 7.5, MICRODIALYSIS, temperature 293K
Resolution 1.76 Å R-free 0.178
1ELM CADMIUM-SUBSTITUTED BOVINE PACREATIC CARBOXYPEPTIDASE A (ALFA-FORM) AT PH 5.5 AND 2 MM CHLORIDE IN MONOCLINIC CRYSTAL FORM. Deposited 2000-03-14 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain P 111–419（309 aa） Fragment：ALFA-FORM
Not recorded CD CADMIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions MICRODIALYSIS；pH 5.5；293 K；Lithium chloride, Tris-HNO3, Cadmium chloride, pH 5.50, MICRODIALYSIS, temperature 293K
Resolution 2.00 Å R-free 0.186
1F57 CARBOXYPEPTIDASE A COMPLEX WITH D-CYSTEINE AT 1.75 A Deposited 2000-06-13 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 111–417（307 aa）
Not recorded ZN ZINC ION × 1 DCY D-CYSTEINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions MICRODIALYSIS；pH 6；291 K；LiCl, MES, pH 6.0, MICRODIALYSIS, temperature 18K
Resolution 1.75 Å R-free 0.164
1HDQ Crystal structure of bovine pancreatic carboxypeptidase A complexed with D-N-hydroxyaminocarbonyl phenylalanine at 2.3 A Deposited 2000-11-17 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 111–417（307 aa）
Not recorded INF D-[(N-HYDROXYAMINO)CARBONYL]PHENYLALANINE × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；pH 7.50
Resolution 2.30 Å R-free 0.174
1HDU Crystal structure of bovine pancreatic carboxypeptidase A complexed with aminocarbonylphenylalanine at 1.75 A Deposited 2000-11-17 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 111–417（307 aa）
Not recorded ZN ZINC ION × 1 ING D-[(AMINO)CARBONYL]PHENYLALANINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；pH 7.50
Resolution 1.75 Å R-free 0.229
1HDU Crystal structure of bovine pancreatic carboxypeptidase A complexed with aminocarbonylphenylalanine at 1.75 A Deposited 2000-11-17 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 111–417（307 aa）
Not recorded ZN ZINC ION × 1 ING D-[(AMINO)CARBONYL]PHENYLALANINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；pH 7.50
Resolution 1.75 Å R-free 0.229
1HDU Crystal structure of bovine pancreatic carboxypeptidase A complexed with aminocarbonylphenylalanine at 1.75 A Deposited 2000-11-17 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 111–417（307 aa）
Not recorded ZN ZINC ION × 1 ING D-[(AMINO)CARBONYL]PHENYLALANINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；pH 7.50
Resolution 1.75 Å R-free 0.229
1HDU Crystal structure of bovine pancreatic carboxypeptidase A complexed with aminocarbonylphenylalanine at 1.75 A Deposited 2000-11-17 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain E 111–417（307 aa）
Not recorded ZN ZINC ION × 1 ING D-[(AMINO)CARBONYL]PHENYLALANINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；pH 7.50
Resolution 1.75 Å R-free 0.229
1HEE Crystal structure of bovine pancreatic carboxypeptidase A complexed with L-N-hydroxyaminocarbonyl phenylalanine at 2.3 A Deposited 2000-11-22 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 111–417（307 aa）
Not recorded ZN ZINC ION × 1 LHY L-[(N-HYDROXYAMINO)CARBONYL]PHENYLALANINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；pH 7.50
Resolution 1.75 Å R-free 0.229
1HEE Crystal structure of bovine pancreatic carboxypeptidase A complexed with L-N-hydroxyaminocarbonyl phenylalanine at 2.3 A Deposited 2000-11-22 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 111–417（307 aa）
Not recorded ZN ZINC ION × 1 LHY L-[(N-HYDROXYAMINO)CARBONYL]PHENYLALANINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；pH 7.50
Resolution 1.75 Å R-free 0.229
1HEE Crystal structure of bovine pancreatic carboxypeptidase A complexed with L-N-hydroxyaminocarbonyl phenylalanine at 2.3 A Deposited 2000-11-22 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 111–417（307 aa）
Not recorded ZN ZINC ION × 1 LHY L-[(N-HYDROXYAMINO)CARBONYL]PHENYLALANINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；pH 7.50
Resolution 1.75 Å R-free 0.229
1HEE Crystal structure of bovine pancreatic carboxypeptidase A complexed with L-N-hydroxyaminocarbonyl phenylalanine at 2.3 A Deposited 2000-11-22 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain E 111–417（307 aa）
Not recorded ZN ZINC ION × 1 LHY L-[(N-HYDROXYAMINO)CARBONYL]PHENYLALANINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；pH 7.50
Resolution 1.75 Å R-free 0.229
1IY7 Crystal Structure of CPA and sulfamide-based inhibitor complex Deposited 2002-07-24 Different construct Different ligand/ion Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 111–417（307 aa）
Not recorded ZN ZINC ION × 1 CXA PHENYLALANINE-N-SULFONAMIDE × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.00 Å R-free 0.208
1M4L STRUCTURE OF NATIVE CARBOXYPEPTIDASE A AT 1.25 RESOLUTION Deposited 2002-07-03 Different construct Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 111–417（307 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.25 Å R-free 0.145
1PYT TERNARY COMPLEX OF PROCARBOXYPEPTIDASE A, PROPROTEINASE E, AND CHYMOTRYPSINOGEN C Deposited 1995-06-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 17–110（94 aa）
Chain B 111–419（309 aa）
Not recorded ZN ZINC ION × 1 CA CALCIUM ION × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.35 Å R-free 0.283
1ZLH Crystal structure of the tick carboxypeptidase inhibitor in complex with bovine carboxypeptidase A Deposited 2005-05-06 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 111–419（309 aa）
Not recorded ZN ZINC ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.2M sodium cacodylate, 0.2M zinc acetate dihydrate, 7%(w/v) PEG 8000, 10%(w/v) dried dioxan, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Resolution 1.70 Å R-free 0.185
2ABZ Crystal structure of C19A/C43A mutant of leech carboxypeptidase inhibitor in complex with bovine carboxypeptidase A Deposited 2005-07-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 111–419（309 aa）
Chain B 111–419（309 aa）
Not recorded ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；1.5M Lithium Sulfate monohydrate, 100mM Tris, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.16 Å R-free 0.234
2CTB THE HIGH RESOLUTION CRYSTAL STRUCTURE OF THE COMPLEX BETWEEN CARBOXYPEPTIDASE A AND L-PHENYL LACTATE Deposited 1993-04-02 Different construct Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 111–417（307 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.50 Å
2CTC THE HIGH RESOLUTION CRYSTAL STRUCTURE OF THE COMPLEX BETWEEN CARBOXYPEPTIDASE A AND L-PHENYL LACTATE Deposited 1993-04-02 Different construct Different ligand/ion Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 111–417（307 aa）
Not recorded ZN ZINC ION × 1 HFA ALPHA-HYDROXY-BETA-PHENYL-PROPIONIC ACID × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.40 Å
3CPA X-RAY CRYSTALLOGRAPHIC INVESTIGATION OF SUBSTRATE BINDING TO CARBOXYPEPTIDASE A AT SUBZERO TEMPERATURE Deposited 1982-03-24 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 111–417（307 aa）
Not recorded GLY GLYCINE × 1 TYR TYROSINE × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions THE COMPLEX WAS PREPARED BY DIFFUSION OF GLY-TYR INTO CPA CRYSTALS. THE OCCUPANCY OF THE GLY-TYR IS APPROXIMATELY FORTY PERCENT.
Resolution 2.00 Å
3FVL Crystallogic studies on the Complex of Carboxypeptidase A with inhibitors using alpha-hydroxy ketone as zinc-binding group Deposited 2009-01-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 111–417（307 aa） Fragment：residues 1-307
Chain C 111–417（307 aa） Fragment：residues 1-307
Chain E 111–417（307 aa） Fragment：residues 1-307
Not recorded ZN ZINC ION × 3 BHK (2R)-2-benzyl-5-hydroxy-4-oxopentanoic acid × 3 X-RAY DIFFRACTION
X-ray crystallization conditions MICRODIALYSIS；pH 7.5；277 K；0.02% glutaraldehyde, 0.15M lithium chloride, pH 7.5, temperature 277K, MICRODIALYSIS
Resolution 1.85 Å R-free 0.238
3FVL Crystallogic studies on the Complex of Carboxypeptidase A with inhibitors using alpha-hydroxy ketone as zinc-binding group Deposited 2009-01-16 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 111–417（307 aa） Fragment：residues 1-307
Not recorded ZN ZINC ION × 1 BHK (2R)-2-benzyl-5-hydroxy-4-oxopentanoic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions MICRODIALYSIS；pH 7.5；277 K；0.02% glutaraldehyde, 0.15M lithium chloride, pH 7.5, temperature 277K, MICRODIALYSIS
Resolution 1.85 Å R-free 0.238
3FVL Crystallogic studies on the Complex of Carboxypeptidase A with inhibitors using alpha-hydroxy ketone as zinc-binding group Deposited 2009-01-16 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 111–417（307 aa） Fragment：residues 1-307
Not recorded ZN ZINC ION × 1 BHK (2R)-2-benzyl-5-hydroxy-4-oxopentanoic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions MICRODIALYSIS；pH 7.5；277 K；0.02% glutaraldehyde, 0.15M lithium chloride, pH 7.5, temperature 277K, MICRODIALYSIS
Resolution 1.85 Å R-free 0.238
3FVL Crystallogic studies on the Complex of Carboxypeptidase A with inhibitors using alpha-hydroxy ketone as zinc-binding group Deposited 2009-01-16 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain E 111–417（307 aa） Fragment：residues 1-307
Not recorded ZN ZINC ION × 1 BHK (2R)-2-benzyl-5-hydroxy-4-oxopentanoic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions MICRODIALYSIS；pH 7.5；277 K；0.02% glutaraldehyde, 0.15M lithium chloride, pH 7.5, temperature 277K, MICRODIALYSIS
Resolution 1.85 Å R-free 0.238
3FX6 X-RAY crystallographic studies on the complex of carboxypeptidase A with the inhibitor using alpha-nitro ketone as the zinc-binding group Deposited 2009-01-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 111–417（307 aa）
Chain C 111–417（307 aa）
Chain E 111–417（307 aa）
Not recorded ZN ZINC ION × 3 BPX (2R)-4,4-dihydroxy-5-nitro-2-(phenylmethyl)pentanoic acid × 3 X-RAY DIFFRACTION
X-ray crystallization conditions MICRODIALYSIS；pH 7.5；277 K；0.15M lithium chloride, 0.02% glutaraldehyde, 0.025M Tris, pH7.5, MICRODIALYSIS, temperature 277K
Resolution 1.85 Å R-free 0.239
3FX6 X-RAY crystallographic studies on the complex of carboxypeptidase A with the inhibitor using alpha-nitro ketone as the zinc-binding group Deposited 2009-01-20 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 111–417（307 aa）
Not recorded ZN ZINC ION × 1 BPX (2R)-4,4-dihydroxy-5-nitro-2-(phenylmethyl)pentanoic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions MICRODIALYSIS；pH 7.5；277 K；0.15M lithium chloride, 0.02% glutaraldehyde, 0.025M Tris, pH7.5, MICRODIALYSIS, temperature 277K
Resolution 1.85 Å R-free 0.239
3FX6 X-RAY crystallographic studies on the complex of carboxypeptidase A with the inhibitor using alpha-nitro ketone as the zinc-binding group Deposited 2009-01-20 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 111–417（307 aa）
Not recorded ZN ZINC ION × 1 BPX (2R)-4,4-dihydroxy-5-nitro-2-(phenylmethyl)pentanoic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions MICRODIALYSIS；pH 7.5；277 K；0.15M lithium chloride, 0.02% glutaraldehyde, 0.025M Tris, pH7.5, MICRODIALYSIS, temperature 277K
Resolution 1.85 Å R-free 0.239
3FX6 X-RAY crystallographic studies on the complex of carboxypeptidase A with the inhibitor using alpha-nitro ketone as the zinc-binding group Deposited 2009-01-20 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain E 111–417（307 aa）
Not recorded ZN ZINC ION × 1 BPX (2R)-4,4-dihydroxy-5-nitro-2-(phenylmethyl)pentanoic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions MICRODIALYSIS；pH 7.5；277 K；0.15M lithium chloride, 0.02% glutaraldehyde, 0.025M Tris, pH7.5, MICRODIALYSIS, temperature 277K
Resolution 1.85 Å R-free 0.239
3KGQ Carboxypeptidase A liganded to an organic small-molecule: conformational changes Deposited 2009-10-29 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 111–419（309 aa）
Not recorded ZN ZINC ION × 1 NA SODIUM ION × 1 CIT CITRIC ACID × 1 ACN ACETONE × 1 FMT FORMIC ACID × 3 GOL GLYCEROL × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；289 K；20% PEG 3350, 0.2M NH4Cl, 0.02M Tris, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Resolution 1.70 Å R-free 0.204
4CPA REFINED CRYSTAL STRUCTURE OF THE POTATO INHIBITOR COMPLEX OF CARBOXYPEPTIDASE A AT 2.5 ANGSTROMS RESOLUTION Deposited 1982-03-24 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 111–417（307 aa）
Not recorded GLY GLYCINE × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.50 Å
4CPA REFINED CRYSTAL STRUCTURE OF THE POTATO INHIBITOR COMPLEX OF CARBOXYPEPTIDASE A AT 2.5 ANGSTROMS RESOLUTION Deposited 1982-03-24 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 111–417（307 aa）
Not recorded GLY GLYCINE × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.50 Å
5CPA REFINED CRYSTAL STRUCTURE OF CARBOXYPEPTIDASE A AT 1.54 ANGSTROMS RESOLUTION. Deposited 1982-05-06 Different construct Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 111–417（307 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.54 Å
6CPA CRYSTAL STRUCTURE OF THE COMPLEX OF CARBOXYPEPTIDASE A WITH A STRONGLY BOUND PHOSPHONATE IN A NEW CRYSTALLINE FORM: COMPARISON WITH STRUCTURES OF OTHER COMPLEXES Deposited 1990-02-15 Different construct Different ligand/ion Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 111–417（307 aa）
Not recorded ZN ZINC ION × 1 ZAF O-(((1R)-((N-PHENYLMETHOXYCARBONYL-L-ALANYL)AMINO)ETHYL)HYDROXYPHOSPHONO)-L-BENZYLACETIC ACID × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.00 Å
7CPA COMPARISON OF THE STRUCTURES OF THREE CARBOXYPEPTIDASE A-PHOSPHONATE COMPLEXES DETERMINED BY X-RAY CRYSTALLOGRAPHY Deposited 1991-05-21 Different construct Different ligand/ion Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 111–417（307 aa）
Not recorded ZN ZINC ION × 1 FVF O-((((N-PHENYL-METHOXY-CARBONYL)-PHENYL ALANYL-CARBONYL)AMINO)-ISOBUTYL)HYDROXY PHOSPHINYL)-3-PHENYLACETIC ACID × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.00 Å
8CPA COMPARISON OF THE STRUCTURES OF THREE CARBOXYPEPTIDASE A-PHOSPHONATE COMPLEXES DETERMINED BY X-RAY CRYSTALLOGRAPHY Deposited 1991-05-21 Different construct Different ligand/ion Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 111–417（307 aa）
Not recorded ZN ZINC ION × 1 AGF O-(((1R)-((N-(PHENYL-METHOXY-CARBONYL)-ALANYL)-AMINO)METHYL)HYDROXYPHOSPHINYL)3-L-PHENYLLACTATE × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.00 Å

29 other PDB entries and 45 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CBPA1_BOVIN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–309； UniProt 111–419

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 1yme

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1yme
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1yme
Deposition date deposition_date1996-07-15
Structure title titleSTRUCTURE OF CARBOXYPEPTIDASE
Keywords keywordsCARBOXYPEPTIDASE, METALLOPROTEINASE, METALLOEXOPROTEINASE; CARBOXYPEPTIDASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier19.41 Å
Radius of gyration Rg (electron density) rg_electron18.07 Å
Forward intensity I(0) i019907700.00
Molecular weight molecular_weight34457.0 kDa
Excluded volume excluded_volume43192 ų
Envelope volume envelope_volume46977 ų
Hydration-shell volume shell_volume21042 ų
Envelope diameter envelope_diameter61.8 Å
Shell Rg shell_rg25.14 Å
Envelope Rg envelope_rg18.35 Å
Shape Rg shape_rg18.04 Å
Total Rg total_rg19.12 Å
Total atoms total_atoms2437
Residues n_residues307
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax63.8 Å
Rg (real space) rg_real19.55 Å
Rg uncertainty (real space) rg_real_error0.14 Å
I(0) (real space) i0_real1.9520e+07
I(0) uncertainty (real space) i0_real_error1.7890e+05
Rg (reciprocal space) rg_reciprocal19.27 Å
I(0) (reciprocal space) i0_reciprocal19910000.0000
Solution quality estimate total_estimate0.6780
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary26.1 Å
Skewness Skewness skewness0.212
Kurtosis Kurtosis kurtosis-0.114
Angular range angular_range— – 0.4100 Å−1
Current regularization parameter α current_alpha7.2170
Highest regularization parameter α highest_alpha7019000.0000
Real-space data points n_real_points72
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.800; Stabil: 0.932; Sysdev: 0.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.645
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1ymea_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.56 — Phosphorylase/hydrolase-like
Superfamily Superfamily superfamilyc.56.5 — Zn-dependent exopeptidases
Family Family familyc.56.5.1 — Pancreatic carboxypeptidases

CATH v4.4 (1 domains)

Domain ID domain_id1ymeA00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology630 — Aminopeptidase
Homologous superfamily homologous superfamily10 — Zn peptidases
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8. Citations (1)

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9. Files and Curves (10)