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1wpx

Crystal structure of carboxypeptidase Y inhibitor complexed with the cognate proteinase

Method: X-RAY DIFFRACTION Dmax: 84.1 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Carboxypeptidase Y

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 112–532 Not recorded Carboxypeptidase Y inhibitor × 1 （P14306） 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

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 1WPX Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1CPY SITE-DIRECTED MUTAGENESIS ON (SERINE) CARBOXYPEPTIDASE Y FROM YEAST. THE SIGNIFICANCE OF THR 60 AND MET 398 IN HYDROLYSIS AND AMINOLYSIS REACTIONS Deposited 1995-03-24 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 112–532（421 aa）
Mutation：E65A, E145A NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.60 Å
1YSC 2.8 ANGSTROMS STRUCTURE OF YEAST SERINE CARBOXYPEPTIDASE Deposited 1994-03-08 Different oligomeric state Different ligand/ion Different experimental conditions 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

Carboxypeptidase Y inhibitor

OrganismNot specified

UniProt P14306

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain B； UniProt 1–219 Non-standard monomer：Yes (specific site not provided by mmCIF) Carboxypeptidase Y × 1 （P00729） 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

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence
UniProt name CPYI_YEAST
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 2–220； UniProt 1–219

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 1wpx

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id1wpx
Deposition date deposition_date2004-09-14
Structure title titleCrystal structure of carboxypeptidase Y inhibitor complexed with the cognate proteinase
Keywords keywords;Carboxypeptidase inhibitor, serine proteinase inhibitor, proteinase-inhibitor complex, phosphatidylethanolamine-binding protein, phospholipid, Hydrolase ;; HYDROLASE
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_guinier26.46 Å
Radius of gyration Rg (electron density) rg_electron25.54 Å
Forward intensity I(0) i082182800.00
Molecular weight molecular_weight70996.0 kDa
Excluded volume excluded_volume88442 ų
Envelope volume envelope_volume101820 ų
Hydration-shell volume shell_volume32725 ų
Envelope diameter envelope_diameter88.2 Å
Shell Rg shell_rg33.42 Å
Envelope Rg envelope_rg25.74 Å
Shape Rg shape_rg25.53 Å
Total Rg total_rg26.37 Å
Total atoms total_atoms5012
Residues n_residues625
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 dmax84.1 Å
Rg (real space) rg_real26.41 Å
Rg uncertainty (real space) rg_real_error0.51 Å
I(0) (real space) i0_real8.2180e+07
I(0) uncertainty (real space) i0_real_error1.2470e+06
Rg (reciprocal space) rg_reciprocal26.43 Å
I(0) (reciprocal space) i0_reciprocal82180000.0000
Solution quality estimate total_estimate0.8984
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary30.8 Å
Skewness Skewness skewness0.322
Kurtosis Kurtosis kurtosis-0.348
Angular range angular_range— – 0.3000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha15760000.0000
Real-space data points n_real_points61
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.899; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.978
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

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7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd1wpxa_
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
Domain ID domain_idd1wpxb1
Class classb — All beta proteins
Fold Fold foldb.17 — PEBP-like
Superfamily Superfamily superfamilyb.17.1 — PEBP-like
Family Family familyb.17.1.1 — Phosphatidylethanolamine binding protein

CATH v4.4 (3 domains)

Domain ID domain_id1wpxA01
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_id1wpxA02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology287 — Helix Hairpins
Homologous superfamily homologous superfamily410 —
Domain ID domain_id1wpxB00
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology280 — Phosphatidylethanolamine-binding Protein
Homologous superfamily homologous superfamily10 — PEBP-like
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8. Citations (1)

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9. Files and Curves (10)