1pyt

TERNARY COMPLEX OF PROCARBOXYPEPTIDASE A, PROPROTEINASE E, AND CHYMOTRYPSINOGEN C

Method: X-RAY DIFFRACTION Dmax: 98.2 Å Quality: EXCELLENT

1. Protein Identity and Related Structures Protein Identity & Related Structures

PROCARBOXYPEPTIDASE A

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 heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain A; UniProt 17–110 Chain B; UniProt 111–419 Not recorded PROPROTEINASE E × 1 (P05805) CHYMOTRYPSINOGEN C × 1 ZN ZINC ION × 1 CA CALCIUM ION × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 2.35 Å R-free 0.283

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.

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, 2
Chains and sequence ranges Author chain A; PDBConstruct 1–94; UniProt 17–110 Author chain B; PDBConstruct 1–309; UniProt 111–419

PROPROTEINASE E

OrganismNot specified

UniProt P05805

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 × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain C; UniProt 1–253 Not recorded PROCARBOXYPEPTIDASE A × 1 (P00730) PROCARBOXYPEPTIDASE A × 1 (P00730) CHYMOTRYPSINOGEN C × 1 ZN ZINC ION × 1 CA CALCIUM ION × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 2.35 Å R-free 0.283

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.

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CAC3_BOVIN
Isoform
PDB entities 3
Chains and sequence ranges Author chain C; PDBConstruct 1–253; UniProt 1–253

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 1pyt

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id1pyt
Deposition date deposition_date1995-06-21
Structure title titleTERNARY COMPLEX OF PROCARBOXYPEPTIDASE A, PROPROTEINASE E, AND CHYMOTRYPSINOGEN C
Keywords keywordsTERNARY COMPLEX (ZYMOGEN), SERINE PROTEINASE, C-TERMINAL PEPTIDASE; TERNARY COMPLEX (ZYMOGEN)
Experimental Method methodX-RAY DIFFRACTION

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier31.43
Radius of gyration Rg (electron density) rg_electron30.69
Forward intensity I(0) i0158341000.00
Molecular weight molecular_weight99681.0 kDa
Excluded volume excluded_volume124310 ų
Envelope volume envelope_volume152200 ų
Hydration-shell volume shell_volume40777 ų
Envelope diameter envelope_diameter98.8
Shell Rg shell_rg38.32
Envelope Rg envelope_rg30.43
Shape Rg shape_rg30.68
Total Rg total_rg31.35
Total atoms total_atoms7030
Residues n_residues877
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −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

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax98.2
Rg (real space) rg_real31.31
Rg uncertainty (real space) rg_real_error0.65
I(0) (real space) i0_real1.5830e+08
I(0) uncertainty (real space) i0_real_error2.2670e+06
Rg (reciprocal space) rg_reciprocal31.37
I(0) (reciprocal space) i0_reciprocal158300000.0000
Solution quality estimate total_estimate0.9090
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary33.4
Skewness Skewness skewness0.168
Kurtosis Kurtosis kurtosis-0.678
Angular range angular_range— – 0.2500 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha63060000.0000
Real-space data points n_real_points51
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.949; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.965

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (7)

7. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd1pyta_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.58 — Ferredoxin-like
Superfamily Superfamily superfamilyd.58.3 — Protease propeptides/inhibitors
Family Family familyd.58.3.1 — Pancreatic carboxypeptidase, activation domain
Domain ID domain_idd1pytb_
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
Domain ID domain_idd1pytc_
Class classb — All beta proteins
Fold Fold foldb.47 — Trypsin-like serine proteases
Superfamily Superfamily superfamilyb.47.1 — Trypsin-like serine proteases
Family Family familyb.47.1.2 — Eukaryotic proteases
Domain ID domain_idd1pytd_
Class classb — All beta proteins
Fold Fold foldb.47 — Trypsin-like serine proteases
Superfamily Superfamily superfamilyb.47.1 — Trypsin-like serine proteases
Family Family familyb.47.1.2 — Eukaryotic proteases

CATH v4.4 (6 domains)

Domain ID domain_id1pytA00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily340 — Metallocarboxypeptidase-like
Domain ID domain_id1pytB00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology630 — Aminopeptidase
Homologous superfamily homologous superfamily10 — Zn peptidases
Domain ID domain_id1pytC01
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology10 — Thrombin, subunit H
Homologous superfamily homologous superfamily10 — Trypsin-like serine proteases
Domain ID domain_id1pytC02
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology10 — Thrombin, subunit H
Homologous superfamily homologous superfamily10 — Trypsin-like serine proteases
Domain ID domain_id1pytD01
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology10 — Thrombin, subunit H
Homologous superfamily homologous superfamily10 — Trypsin-like serine proteases
Domain ID domain_id1pytD02
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology10 — Thrombin, subunit H
Homologous superfamily homologous superfamily10 — Trypsin-like serine proteases

8. Citations (2)

9. Files and Curves (10)