1p2q

Structural consequences of accommodation of four non-cognate amino-acid residues in the S1 pocket of bovine trypsin and chymotrypsin

Method: X-RAY DIFFRACTION Dmax: 96.7 Å Quality: GOOD

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

Chymotrypsinogen 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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 1–245 Not recorded Pancreatic trypsin inhibitor × 1 (P00974) SO4 SULFATE ION × 7 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.8;298 K;50% ammonium sulfate, 0.1M Tris, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 1.80 Å R-free 0.221
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain C; UniProt 1–245 Not recorded Pancreatic trypsin inhibitor × 1 (P00974) SO4 SULFATE ION × 3 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.8;298 K;50% ammonium sulfate, 0.1M Tris, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 1.80 Å R-free 0.221
3 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain A; UniProt 1–245 Chain C; UniProt 1–245 Not recorded Pancreatic trypsin inhibitor × 2 (P00974) SO4 SULFATE ION × 10 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.8;298 K;50% ammonium sulfate, 0.1M Tris, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 1.80 Å R-free 0.221
4 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 1–245 Not recorded Pancreatic trypsin inhibitor × 1 (P00974) SO4 SULFATE ION × 4 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.8;298 K;50% ammonium sulfate, 0.1M Tris, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 1.80 Å R-free 0.221
5 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain C; UniProt 1–245 Not recorded Pancreatic trypsin inhibitor × 1 (P00974) SO4 SULFATE ION × 6 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.8;298 K;50% ammonium sulfate, 0.1M Tris, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 1.80 Å R-free 0.221

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 173 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CTRA_BOVIN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–245; UniProt 1–245 Author chain C; PDBConstruct 1–245; UniProt 1–245

Pancreatic trypsin inhibitor

Bos taurus

UniProt P00974

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 36–93 Mutation:K15F, M52L Chymotrypsinogen A × 1 (P00766) SO4 SULFATE ION × 7 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.8;298 K;50% ammonium sulfate, 0.1M Tris, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 1.80 Å R-free 0.221
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain D; UniProt 36–93 Mutation:K15F, M52L Chymotrypsinogen A × 1 (P00766) SO4 SULFATE ION × 3 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.8;298 K;50% ammonium sulfate, 0.1M Tris, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 1.80 Å R-free 0.221
3 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain B; UniProt 36–93 Chain D; UniProt 36–93 Mutation:K15F, M52L Chymotrypsinogen A × 2 (P00766) SO4 SULFATE ION × 10 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.8;298 K;50% ammonium sulfate, 0.1M Tris, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 1.80 Å R-free 0.221
4 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain D; UniProt 36–93 Mutation:K15F, M52L Chymotrypsinogen A × 1 (P00766) SO4 SULFATE ION × 4 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.8;298 K;50% ammonium sulfate, 0.1M Tris, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 1.80 Å R-free 0.221
5 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain B; UniProt 36–93 Mutation:K15F, M52L Chymotrypsinogen A × 1 (P00766) SO4 SULFATE ION × 6 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.8;298 K;50% ammonium sulfate, 0.1M Tris, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 1.80 Å R-free 0.221

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.

123 other PDB entries and 261 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name BPT1_BOVIN
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 1–58; UniProt 36–93 Author chain D; PDBConstruct 1–58; UniProt 36–93

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 1p2q

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1p2q
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1p2q
Deposition date deposition_date2003-04-15
Structure title titleStructural consequences of accommodation of four non-cognate amino-acid residues in the S1 pocket of bovine trypsin and chymotrypsin
Keywords keywords;trypsin; chymotrypsin; serine proteinase; bovine pancreatic trypsin inhibitor; protein-protein interaction; non-cognate binding; S1 pocket; primary specificity; crystal structure, hydrolase-hydrolase inhibitor COMPLEX ;; hydrolase/hydrolase inhibitor
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier29.74
Radius of gyration Rg (electron density) rg_electron29.65
Forward intensity I(0) i072043000.00
Molecular weight molecular_weight64333.0 kDa
Excluded volume excluded_volume79472 ų
Envelope volume envelope_volume96434 ų
Hydration-shell volume shell_volume28426 ų
Envelope diameter envelope_diameter102.6
Shell Rg shell_rg35.21
Envelope Rg envelope_rg29.51
Shape Rg shape_rg29.64
Total Rg total_rg30.19
Total atoms total_atoms4488
Residues n_residues594
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 dmax96.7
Rg (real space) rg_real29.95
Rg uncertainty (real space) rg_real_error0.75
I(0) (real space) i0_real7.2040e+07
I(0) uncertainty (real space) i0_real_error9.7840e+05
Rg (reciprocal space) rg_reciprocal29.87
I(0) (reciprocal space) i0_reciprocal72040000.0000
Solution quality estimate total_estimate0.8335
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary94.8
Skewness Skewness skewness0.456
Kurtosis Kurtosis kurtosis-0.620
Angular range angular_range— – 0.2650 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha25970000.0000
Real-space data points n_real_points54
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.727; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.807; Smooth: 0.842

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd1p2qa_
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_idd1p2qb_
Class classg — Small proteins
Fold Fold foldg.8 — BPTI-like
Superfamily Superfamily superfamilyg.8.1 — BPTI-like
Family Family familyg.8.1.1 — Small Kunitz-type inhibitors & BPTI-like toxins
Domain ID domain_idd1p2qc_
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_idd1p2qd_
Class classg — Small proteins
Fold Fold foldg.8 — BPTI-like
Superfamily Superfamily superfamilyg.8.1 — BPTI-like
Family Family familyg.8.1.1 — Small Kunitz-type inhibitors & BPTI-like toxins

CATH v4.4 (6 domains)

Domain ID domain_id1p2qA01
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology10 — Thrombin, subunit H
Homologous superfamily homologous superfamily10 — Trypsin-like serine proteases
Domain ID domain_id1p2qA02
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology10 — Thrombin, subunit H
Homologous superfamily homologous superfamily10 — Trypsin-like serine proteases
Domain ID domain_id1p2qB00
Class class4 — Few Secondary Structures
Architecture architecture10 — Irregular
Topology topology410 — Factor Xa Inhibitor
Homologous superfamily homologous superfamily10 — Pancreatic trypsin inhibitor Kunitz domain
Domain ID domain_id1p2qC01
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology10 — Thrombin, subunit H
Homologous superfamily homologous superfamily10 — Trypsin-like serine proteases
Domain ID domain_id1p2qC02
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology10 — Thrombin, subunit H
Homologous superfamily homologous superfamily10 — Trypsin-like serine proteases
Domain ID domain_id1p2qD00
Class class4 — Few Secondary Structures
Architecture architecture10 — Irregular
Topology topology410 — Factor Xa Inhibitor
Homologous superfamily homologous superfamily10 — Pancreatic trypsin inhibitor Kunitz domain

8. Citations (1)

9. Files and Curves (10)