3u1j

Aprotinin bound to Dengue virus protease

Method: X-RAY DIFFRACTION Dmax: 64.7 Å Quality: GOOD

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

Serine protease subunit NS2B

Dengue virus 3

UniProt Q5UB51

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 × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain A; UniProt 1393–1438 Chain B; UniProt 1474–1655 Fragment:UNP residues 1393-1438 Fragment:UNP residues 1474-1655 Pancreatic trypsin inhibitor × 1 (P00974) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 6.5;291 K;0.1M MES pH 6.5, 30% PEG 4000, VAPOR DIFFUSION, SITTING DROP, temperature 291K Resolution 1.80 Å R-free 0.204

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 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name POLG_DEN3I
Isoform
PDB entities 1, 2
Chains and sequence ranges Author chain A; PDBConstruct 6–51; UniProt 1393–1438 Author chain B; PDBConstruct 10–191; UniProt 1474–1655

Pancreatic trypsin inhibitor

OrganismNot specified

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 × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain E; UniProt 36–93 Fragment:UNP residues 36-93 Serine protease subunit NS2B × 1 (Q5UB51) Serine protease NS3 × 1 (Q5UB51) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 6.5;291 K;0.1M MES pH 6.5, 30% PEG 4000, VAPOR DIFFUSION, SITTING DROP, temperature 291K Resolution 1.80 Å R-free 0.204

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 265 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name BPT1_BOVIN
Isoform
PDB entities 3
Chains and sequence ranges Author chain E; 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 3u1j

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3u1j
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3u1j
Deposition date deposition_date2011-09-30
Structure title titleAprotinin bound to Dengue virus protease
Keywords keywordsSERINE PROTEASE, BOVINE PANCREATIC TRYPSIN INHIBITOR, ER MEMBRANE, 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_guinier19.95
Radius of gyration Rg (electron density) rg_electron18.88
Forward intensity I(0) i012873400.00
Molecular weight molecular_weight26368.0 kDa
Excluded volume excluded_volume32823 ų
Envelope volume envelope_volume39712 ų
Hydration-shell volume shell_volume18008 ų
Envelope diameter envelope_diameter66.5
Shell Rg shell_rg24.68
Envelope Rg envelope_rg19.40
Shape Rg shape_rg18.84
Total Rg total_rg19.85
Total atoms total_atoms1856
Residues n_residues242
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 dmax64.7
Rg (real space) rg_real19.92
Rg uncertainty (real space) rg_real_error0.47
I(0) (real space) i0_real1.2870e+07
I(0) uncertainty (real space) i0_real_error1.7390e+05
Rg (reciprocal space) rg_reciprocal19.93
I(0) (reciprocal space) i0_reciprocal12870000.0000
Solution quality estimate total_estimate0.8204
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary23.7
Skewness Skewness skewness0.296
Kurtosis Kurtosis kurtosis-0.429
Angular range angular_range— – 0.4000 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha2548000.0000
Real-space data points n_real_points72
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.893; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.984; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd3u1jb_
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.47.1.3 — Viral proteases
Domain ID domain_idd3u1je_
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 (3 domains)

Domain ID domain_id3u1jB01
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology10 — Thrombin, subunit H
Homologous superfamily homologous superfamily120
Domain ID domain_id3u1jB02
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology10 — Thrombin, subunit H
Homologous superfamily homologous superfamily10 — Trypsin-like serine proteases
Domain ID domain_id3u1jE00
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)