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1cpy

SITE-DIRECTED MUTAGENESIS ON (SERINE) CARBOXYPEPTIDASE Y FROM YEAST. THE SIGNIFICANCE OF THR 60 AND MET 398 IN HYDROLYSIS AND AMINOLYSIS REACTIONS

Method: X-RAY DIFFRACTION Dmax: 66.1 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

SERINE CARBOXYPEPTIDASE

OrganismNot specified

UniProt P00729

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 112–532 Mutation：E65A, E145A NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 2.60 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 1CPY Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1WPX Crystal structure of carboxypeptidase Y inhibitor complexed with the cognate proteinase Deposited 2004-09-14 Different mutation/modification 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 112–532（421 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.7；298 K；0.1M Sodium acetate, 1.95M ammonium sulfate, pH 4.7, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.70 Å R-free 0.225
1YSC 2.8 ANGSTROMS STRUCTURE OF YEAST SERINE CARBOXYPEPTIDASE Deposited 1994-03-08 Different mutation/modification Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 112–532（421 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.80 Å

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CBPY_YEAST
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–421； UniProt 112–532

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 1cpy

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id1cpy
Deposition date deposition_date1995-03-24
Structure title titleSITE-DIRECTED MUTAGENESIS ON (SERINE) CARBOXYPEPTIDASE Y FROM YEAST. THE SIGNIFICANCE OF THR 60 AND MET 398 IN HYDROLYSIS AND AMINOLYSIS REACTIONS
Keywords keywordsHYDROLASE (CARBOXYPEPTIDASE); HYDROLASE (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_guinier21.87 Å
Radius of gyration Rg (electron density) rg_electron20.49 Å
Forward intensity I(0) i036876800.00
Molecular weight molecular_weight46468.0 kDa
Excluded volume excluded_volume57669 ų
Envelope volume envelope_volume65925 ų
Hydration-shell volume shell_volume25815 ų
Envelope diameter envelope_diameter70.4 Å
Shell Rg shell_rg28.05 Å
Envelope Rg envelope_rg20.72 Å
Shape Rg shape_rg20.48 Å
Total Rg total_rg21.41 Å
Total atoms total_atoms3287
Residues n_residues421
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 dmax66.1 Å
Rg (real space) rg_real21.67 Å
Rg uncertainty (real space) rg_real_error0.29 Å
I(0) (real space) i0_real3.6880e+07
I(0) uncertainty (real space) i0_real_error4.0810e+05
Rg (reciprocal space) rg_reciprocal21.71 Å
I(0) (reciprocal space) i0_reciprocal36880000.0000
Solution quality estimate total_estimate0.9001
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary29.6 Å
Skewness Skewness skewness0.071
Kurtosis Kurtosis kurtosis-0.470
Angular range angular_range— – 0.3650 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha7265000.0000
Real-space data points n_real_points68
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.917; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.980; Smooth: 0.966
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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) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1cpya_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.69 — alpha/beta-Hydrolases
Superfamily Superfamily superfamilyc.69.1 — alpha/beta-Hydrolases
Family Family familyc.69.1.5 — Serine carboxypeptidase-like

CATH v4.4 (2 domains)

Domain ID domain_id1cpyA01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1820 — Alpha/Beta hydrolase fold, catalytic domain
Domain ID domain_id1cpyA02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology287 — Helix Hairpins
Homologous superfamily homologous superfamily410 —
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8. Citations (2)

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9. Files and Curves (10)