6di8

Crystal structure of bovine alpha-chymotrypsin in space group P65

Method: X-RAY DIFFRACTION Dmax: 87.5 Å Quality: EXCELLENT

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

Chymotrypsin A chain A

OrganismNot specified

UniProt P00766

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 homooligomer Homooligomer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain A; UniProt 1–13 Chain B; UniProt 16–146 Chain C; UniProt 149–245 Not recorded SO4 SULFATE ION × 5 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;289 K;Protein (lyophilized powder, Worthington, code: CDTLCK) was dissolved in 0.1 M HEPES (pH 7.0) to a final concentration of 20mg/mL. Crystallisation condition was 2 M ammonium sulphate, with equal volume (1 uL) of protein and reservoir solution in the drop Resolution 1.86 Å R-free 0.225
2 Protein homooligomer Homooligomer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain D; UniProt 1–13 Chain E; UniProt 16–146 Chain F; UniProt 149–245 Not recorded SO4 SULFATE ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;289 K;Protein (lyophilized powder, Worthington, code: CDTLCK) was dissolved in 0.1 M HEPES (pH 7.0) to a final concentration of 20mg/mL. Crystallisation condition was 2 M ammonium sulphate, with equal volume (1 uL) of protein and reservoir solution in the drop Resolution 1.86 Å R-free 0.225
3 Protein homooligomer Homooligomer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain G; UniProt 1–13 Chain H; UniProt 16–146 Chain I; UniProt 149–245 Not recorded SO4 SULFATE ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;289 K;Protein (lyophilized powder, Worthington, code: CDTLCK) was dissolved in 0.1 M HEPES (pH 7.0) to a final concentration of 20mg/mL. Crystallisation condition was 2 M ammonium sulphate, with equal volume (1 uL) of protein and reservoir solution in the drop Resolution 1.86 Å R-free 0.225
4 Protein homooligomer Homooligomer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain J; UniProt 1–13 Chain K; UniProt 16–146 Chain L; UniProt 149–245 Not recorded SO4 SULFATE ION × 4 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;289 K;Protein (lyophilized powder, Worthington, code: CDTLCK) was dissolved in 0.1 M HEPES (pH 7.0) to a final concentration of 20mg/mL. Crystallisation condition was 2 M ammonium sulphate, with equal volume (1 uL) of protein and reservoir solution in the drop Resolution 1.86 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.

91 other PDB entries and 174 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CTRA_BOVIN
Isoform
PDB entities 1, 2, 3
Chains and sequence ranges Author chain A; PDBConstruct 1–13; UniProt 1–13 Author chain D; PDBConstruct 1–13; UniProt 1–13 Author chain G; PDBConstruct 1–13; UniProt 1–13 Author chain J; PDBConstruct 1–13; UniProt 1–13 Author chain B; PDBConstruct 1–131; UniProt 16–146 Author chain E; PDBConstruct 1–131; UniProt 16–146 Author chain H; PDBConstruct 1–131; UniProt 16–146 Author chain K; PDBConstruct 1–131; UniProt 16–146 Author chain C; PDBConstruct 1–97; UniProt 149–245 Author chain F; PDBConstruct 1–97; UniProt 149–245 Author chain I; PDBConstruct 1–97; UniProt 149–245 Author chain L; PDBConstruct 1–97; UniProt 149–245

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 6di8

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6di8
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6di8
Deposition date deposition_date2018-05-23
Structure title titleCrystal structure of bovine alpha-chymotrypsin in space group P65
Keywords keywordsTrypsin-like serine protease, endopeptidase, HYDROLASE; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier29.70
Radius of gyration Rg (electron density) rg_electron28.55
Forward intensity I(0) i0175426000.00
Molecular weight molecular_weight101810.0 kDa
Excluded volume excluded_volume126120 ų
Envelope volume envelope_volume152060 ų
Hydration-shell volume shell_volume42828 ų
Envelope diameter envelope_diameter90.8
Shell Rg shell_rg37.22
Envelope Rg envelope_rg28.48
Shape Rg shape_rg28.49
Total Rg total_rg29.52
Total atoms total_atoms7113
Residues n_residues964
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 dmax87.5
Rg (real space) rg_real29.49
Rg uncertainty (real space) rg_real_error0.32
I(0) (real space) i0_real1.7540e+08
I(0) uncertainty (real space) i0_real_error2.1490e+06
Rg (reciprocal space) rg_reciprocal29.58
I(0) (reciprocal space) i0_reciprocal175400000.0000
Solution quality estimate total_estimate0.9083
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary41.3
Skewness Skewness skewness0.035
Kurtosis Kurtosis kurtosis-0.617
Angular range angular_range— – 0.2650 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha70080000.0000
Real-space data points n_real_points54
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.962; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.980; Smooth: 0.937

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

Domain ID domain_id6di8B00
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology10 — Thrombin, subunit H
Homologous superfamily homologous superfamily10 — Trypsin-like serine proteases
Domain ID domain_id6di8C00
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology10 — Thrombin, subunit H
Homologous superfamily homologous superfamily10 — Trypsin-like serine proteases
Domain ID domain_id6di8E00
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology10 — Thrombin, subunit H
Homologous superfamily homologous superfamily10 — Trypsin-like serine proteases
Domain ID domain_id6di8F00
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology10 — Thrombin, subunit H
Homologous superfamily homologous superfamily10 — Trypsin-like serine proteases
Domain ID domain_id6di8H00
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology10 — Thrombin, subunit H
Homologous superfamily homologous superfamily10 — Trypsin-like serine proteases
Domain ID domain_id6di8I00
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology10 — Thrombin, subunit H
Homologous superfamily homologous superfamily10 — Trypsin-like serine proteases
Domain ID domain_id6di8K00
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology10 — Thrombin, subunit H
Homologous superfamily homologous superfamily10 — Trypsin-like serine proteases
Domain ID domain_id6di8L00
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology10 — Thrombin, subunit H
Homologous superfamily homologous superfamily10 — Trypsin-like serine proteases

8. Citations (1)

9. Files and Curves (10)