2hd0

Structure of the catalytic domain of hepatitis C virus NS2

Method: X-RAY DIFFRACTION Dmax: 135.2 Å Quality: GOOD

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

Protease NS2-3 (p23)

Hepatitis C virus

UniProt P27958

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 × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 902–1025 Chain B; UniProt 902–1025 Fragment:protease domain of NS2 BOG octyl beta-D-glucopyranoside × 4 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8.5;277 K;0.1 M Tris pH 8.5 0.8 M Ammonium Acetate 0.25 M Lithium Chloride 12% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K Resolution 2.28 Å R-free 0.268
2 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain C; UniProt 902–1025 Chain D; UniProt 902–1025 Fragment:protease domain of NS2 BOG octyl beta-D-glucopyranoside × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8.5;277 K;0.1 M Tris pH 8.5 0.8 M Ammonium Acetate 0.25 M Lithium Chloride 12% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K Resolution 2.28 Å R-free 0.268
3 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain E; UniProt 902–1025 Chain F; UniProt 902–1025 Fragment:protease domain of NS2 BOG octyl beta-D-glucopyranoside × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8.5;277 K;0.1 M Tris pH 8.5 0.8 M Ammonium Acetate 0.25 M Lithium Chloride 12% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K Resolution 2.28 Å R-free 0.268
4 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain G; UniProt 902–1025 Chain H; UniProt 902–1025 Fragment:protease domain of NS2 BOG octyl beta-D-glucopyranoside × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8.5;277 K;0.1 M Tris pH 8.5 0.8 M Ammonium Acetate 0.25 M Lithium Chloride 12% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K Resolution 2.28 Å R-free 0.268
5 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain I; UniProt 902–1025 Chain J; UniProt 902–1025 Fragment:protease domain of NS2 BOG octyl beta-D-glucopyranoside × 2 DMU DECYL-BETA-D-MALTOPYRANOSIDE × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8.5;277 K;0.1 M Tris pH 8.5 0.8 M Ammonium Acetate 0.25 M Lithium Chloride 12% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K Resolution 2.28 Å R-free 0.268
6 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain K; UniProt 902–1025 Chain L; UniProt 902–1025 Fragment:protease domain of NS2 BOG octyl beta-D-glucopyranoside × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8.5;277 K;0.1 M Tris pH 8.5 0.8 M Ammonium Acetate 0.25 M Lithium Chloride 12% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K Resolution 2.28 Å R-free 0.268

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.

26 other PDB entries and 38 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name POLG_HCVH
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 2–128; UniProt 902–1025 Author chain B; PDBConstruct 2–128; UniProt 902–1025 Author chain C; PDBConstruct 2–128; UniProt 902–1025 Author chain D; PDBConstruct 2–128; UniProt 902–1025 Author chain E; PDBConstruct 2–128; UniProt 902–1025 Author chain F; PDBConstruct 2–128; UniProt 902–1025 Author chain G; PDBConstruct 2–128; UniProt 902–1025 Author chain H; PDBConstruct 2–128; UniProt 902–1025 Author chain I; PDBConstruct 2–128; UniProt 902–1025 Author chain J; PDBConstruct 2–128; UniProt 902–1025 Author chain K; PDBConstruct 2–128; UniProt 902–1025 Author chain L; PDBConstruct 2–128; UniProt 902–1025

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 2hd0

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2hd0
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2hd0
Deposition date deposition_date2006-06-19
Structure title titleStructure of the catalytic domain of hepatitis C virus NS2
Keywords keywordsCysteine Protease, Dimer, Composite Active Site, Hydrolase; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier42.43
Radius of gyration Rg (electron density) rg_electron42.01
Forward intensity I(0) i0380631000.00
Molecular weight molecular_weight167260.0 kDa
Excluded volume excluded_volume213160 ų
Envelope volume envelope_volume298580 ų
Hydration-shell volume shell_volume60927 ų
Envelope diameter envelope_diameter139.3
Shell Rg shell_rg45.86
Envelope Rg envelope_rg40.72
Shape Rg shape_rg42.02
Total Rg total_rg42.18
Total atoms total_atoms11754
Residues n_residues1525
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 dmax135.2
Rg (real space) rg_real42.52
Rg uncertainty (real space) rg_real_error1.07
I(0) (real space) i0_real3.8060e+08
I(0) uncertainty (real space) i0_real_error6.7200e+06
Rg (reciprocal space) rg_reciprocal42.43
I(0) (reciprocal space) i0_reciprocal380600000.0000
Solution quality estimate total_estimate0.8333
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary47.5
Skewness Skewness skewness0.415
Kurtosis Kurtosis kurtosis-0.427
Angular range angular_range— – 0.1850 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha116000000.0000
Real-space data points n_real_points38
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.782; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.483

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 24 domains

CATH v4.4 (24 domains)

Domain ID domain_id2hd0A01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1280 — Monooxygenase
Homologous superfamily homologous superfamily150 — Hepatitis C virus non-structural protein NS2, N-terminal domain
Domain ID domain_id2hd0A02
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology30 — SH3 type barrels.
Homologous superfamily homologous superfamily710 — Hepatitis C virus non-structural protein NS2, C-terminal domain
Domain ID domain_id2hd0B01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1280 — Monooxygenase
Homologous superfamily homologous superfamily150 — Hepatitis C virus non-structural protein NS2, N-terminal domain
Domain ID domain_id2hd0B02
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology30 — SH3 type barrels.
Homologous superfamily homologous superfamily710 — Hepatitis C virus non-structural protein NS2, C-terminal domain
Domain ID domain_id2hd0C01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1280 — Monooxygenase
Homologous superfamily homologous superfamily150 — Hepatitis C virus non-structural protein NS2, N-terminal domain
Domain ID domain_id2hd0C02
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology30 — SH3 type barrels.
Homologous superfamily homologous superfamily710 — Hepatitis C virus non-structural protein NS2, C-terminal domain
Domain ID domain_id2hd0D01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1280 — Monooxygenase
Homologous superfamily homologous superfamily150 — Hepatitis C virus non-structural protein NS2, N-terminal domain
Domain ID domain_id2hd0D02
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology30 — SH3 type barrels.
Homologous superfamily homologous superfamily710 — Hepatitis C virus non-structural protein NS2, C-terminal domain
Domain ID domain_id2hd0E01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1280 — Monooxygenase
Homologous superfamily homologous superfamily150 — Hepatitis C virus non-structural protein NS2, N-terminal domain
Domain ID domain_id2hd0E02
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology30 — SH3 type barrels.
Homologous superfamily homologous superfamily710 — Hepatitis C virus non-structural protein NS2, C-terminal domain
Domain ID domain_id2hd0F01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1280 — Monooxygenase
Homologous superfamily homologous superfamily150 — Hepatitis C virus non-structural protein NS2, N-terminal domain
Domain ID domain_id2hd0F02
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology30 — SH3 type barrels.
Homologous superfamily homologous superfamily710 — Hepatitis C virus non-structural protein NS2, C-terminal domain
Domain ID domain_id2hd0G01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1280 — Monooxygenase
Homologous superfamily homologous superfamily150 — Hepatitis C virus non-structural protein NS2, N-terminal domain
Domain ID domain_id2hd0G02
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology30 — SH3 type barrels.
Homologous superfamily homologous superfamily710 — Hepatitis C virus non-structural protein NS2, C-terminal domain
Domain ID domain_id2hd0H01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1280 — Monooxygenase
Homologous superfamily homologous superfamily150 — Hepatitis C virus non-structural protein NS2, N-terminal domain
Domain ID domain_id2hd0H02
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology30 — SH3 type barrels.
Homologous superfamily homologous superfamily710 — Hepatitis C virus non-structural protein NS2, C-terminal domain
Domain ID domain_id2hd0I01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1280 — Monooxygenase
Homologous superfamily homologous superfamily150 — Hepatitis C virus non-structural protein NS2, N-terminal domain
Domain ID domain_id2hd0I02
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology30 — SH3 type barrels.
Homologous superfamily homologous superfamily710 — Hepatitis C virus non-structural protein NS2, C-terminal domain
Domain ID domain_id2hd0J01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1280 — Monooxygenase
Homologous superfamily homologous superfamily150 — Hepatitis C virus non-structural protein NS2, N-terminal domain
Domain ID domain_id2hd0J02
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology30 — SH3 type barrels.
Homologous superfamily homologous superfamily710 — Hepatitis C virus non-structural protein NS2, C-terminal domain
Domain ID domain_id2hd0K01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1280 — Monooxygenase
Homologous superfamily homologous superfamily150 — Hepatitis C virus non-structural protein NS2, N-terminal domain
Domain ID domain_id2hd0K02
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology30 — SH3 type barrels.
Homologous superfamily homologous superfamily710 — Hepatitis C virus non-structural protein NS2, C-terminal domain
Domain ID domain_id2hd0L01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1280 — Monooxygenase
Homologous superfamily homologous superfamily150 — Hepatitis C virus non-structural protein NS2, N-terminal domain
Domain ID domain_id2hd0L02
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology30 — SH3 type barrels.
Homologous superfamily homologous superfamily710 — Hepatitis C virus non-structural protein NS2, C-terminal domain

8. Citations (1)

9. Files and Curves (10)