2qn5

Crystal Structure and Functional Study of the Bowman-Birk Inhibitor from Rice Bran in Complex with Bovine Trypsin

Method: X-RAY DIFFRACTION Dmax: 76.9 Å Quality: GOOD

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

Bowman-Birk type bran trypsin inhibitor

OrganismNot specified

UniProt Q0JR25

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 119–251 Not recorded Cationic trypsin × 1 (P00760) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7;293 K;11% PEG6000, 0.1M HEPES , pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 3.00 Å R-free 0.322

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 IBBR_ORYSJ
Isoform
PDB entities 1
Chains and sequence ranges Author chain B; PDBConstruct 1–133; UniProt 119–251

Cationic trypsin

OrganismNot specified

UniProt P00760

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 T; UniProt 21–243 Not recorded Bowman-Birk type bran trypsin inhibitor × 1 (Q0JR25) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7;293 K;11% PEG6000, 0.1M HEPES , pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 3.00 Å R-free 0.322

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.

608 other PDB entries and 770 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TRY1_BOVIN
Isoform
PDB entities 2
Chains and sequence ranges Author chain T; PDBConstruct 1–223; UniProt 21–243

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 2qn5

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2qn5
Download Download

2. Structure Basics 2. Structure Basics

Entry ID entry_id2qn5
Deposition date deposition_date2007-07-18
Structure title titleCrystal Structure and Functional Study of the Bowman-Birk Inhibitor from Rice Bran in Complex with Bovine Trypsin
Keywords keywords;RBTI, Bowman-Birk Inhibitor, monocotyledonous plant, reactive-site loop, protease-inhibitor, plant-pest systems, Protease inhibitor, Serine protease inhibitor, Calcium, Digestion, Hydrolase, Metal-binding, Secreted, Zymogen, Hydrolase inhibitor-Hydrolase COMPLEX, HETERO-DIMER ;; Hydrolase inhibitor/Hydrolase
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier22.30
Radius of gyration Rg (electron density) rg_electron21.40
Forward intensity I(0) i024741900.00
Molecular weight molecular_weight35716.0 kDa
Excluded volume excluded_volume43772 ų
Envelope volume envelope_volume55050 ų
Hydration-shell volume shell_volume21943 ų
Envelope diameter envelope_diameter79.1
Shell Rg shell_rg27.71
Envelope Rg envelope_rg21.97
Shape Rg shape_rg21.35
Total Rg total_rg22.34
Total atoms total_atoms2483
Residues n_residues333
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 dmax76.9
Rg (real space) rg_real22.32
Rg uncertainty (real space) rg_real_error0.68
I(0) (real space) i0_real2.4740e+07
I(0) uncertainty (real space) i0_real_error3.8850e+05
Rg (reciprocal space) rg_reciprocal22.31
I(0) (reciprocal space) i0_reciprocal24740000.0000
Solution quality estimate total_estimate0.8712
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary25.6
Skewness Skewness skewness0.412
Kurtosis Kurtosis kurtosis-0.176
Angular range angular_range— – 0.3550 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha4439000.0000
Real-space data points n_real_points67
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.790; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.974; Smooth: 0.977

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (3 domains)

Domain ID domain_idd2qn5b1
Class classg — Small proteins
Fold Fold foldg.3 — Knottins (small inhibitors, toxins, lectins)
Superfamily Superfamily superfamilyg.3.13 — Bowman-Birk inhibitor, BBI
Family Family familyg.3.13.0 — automated matches
Domain ID domain_idd2qn5b2
Class classg — Small proteins
Fold Fold foldg.3 — Knottins (small inhibitors, toxins, lectins)
Superfamily Superfamily superfamilyg.3.13 — Bowman-Birk inhibitor, BBI
Family Family familyg.3.13.0 — automated matches
Domain ID domain_idd2qn5t_
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 (4 domains)

Domain ID domain_id2qn5B01
Class class2 — Mainly Beta
Architecture architecture10 — Ribbon
Topology topology69 — Cysteine Protease (Bromelain) Inhibitor, subunit H
Homologous superfamily homologous superfamily10 — Cysteine Protease (Bromelain) Inhibitor, subunit H
Domain ID domain_id2qn5B02
Class class2 — Mainly Beta
Architecture architecture10 — Ribbon
Topology topology69 — Cysteine Protease (Bromelain) Inhibitor, subunit H
Homologous superfamily homologous superfamily10 — Cysteine Protease (Bromelain) Inhibitor, subunit H
Domain ID domain_id2qn5T01
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology10 — Thrombin, subunit H
Homologous superfamily homologous superfamily10 — Trypsin-like serine proteases
Domain ID domain_id2qn5T02
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)