1n1l

CRYSTAL STRUCTURE OF HCV NS3 PROTEASE DOMAIN:NS4A PEPTIDE COMPLEX WITH COVALENTLY BOUND INHIBITOR (GW472467X)

Method: X-RAY DIFFRACTION Dmax: 75.6 Å Quality: GOOD

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

HCV NS3 SERINE PROTEASE

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 1026–1205 Fragment:Protease domain Mutation:A164T NS4A COFACTOR × 1 ZN ZINC ION × 1 TRL {1-[2-(1-FORMYL-PROPYL)-3-METHANESULFONYLAMINO-PYRROLIDINE-1-CARBONYL]-2-METHYL-PROPYL}-CARBAMIC ACID TERT-BUTYL ESTER × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 6.5;277 K;Inhibitor soaked into crystal generated according to Kim et al. (1996) Cell, 87, 343-355, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277.0K Resolution 2.60 Å R-free 0.220
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain B; UniProt 1026–1205 Fragment:Protease domain Mutation:A164T NS4A COFACTOR × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 6.5;277 K;Inhibitor soaked into crystal generated according to Kim et al. (1996) Cell, 87, 343-355, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277.0K Resolution 2.60 Å R-free 0.220
3 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain A; UniProt 1026–1205 Chain B; UniProt 1026–1205 Fragment:Protease domain Mutation:A164T NS4A COFACTOR × 2 ZN ZINC ION × 2 TRL {1-[2-(1-FORMYL-PROPYL)-3-METHANESULFONYLAMINO-PYRROLIDINE-1-CARBONYL]-2-METHYL-PROPYL}-CARBAMIC ACID TERT-BUTYL ESTER × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 6.5;277 K;Inhibitor soaked into crystal generated according to Kim et al. (1996) Cell, 87, 343-355, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277.0K Resolution 2.60 Å R-free 0.220

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 41 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 11–190; UniProt 1026–1205 Author chain B; PDBConstruct 11–190; UniProt 1026–1205

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 1n1l

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1n1l
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1n1l
Deposition date deposition_date2002-10-18
Structure title titleCRYSTAL STRUCTURE OF HCV NS3 PROTEASE DOMAIN:NS4A PEPTIDE COMPLEX WITH COVALENTLY BOUND INHIBITOR (GW472467X)
Keywords keywordsVIRAL PROTEIN, SERINE PROTEASE, NONSTRUCTURAL PROTEINS, COFACTOR PEPTIDE, HELICASE, INHIBITOR; VIRAL PROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier23.09
Radius of gyration Rg (electron density) rg_electron22.35
Forward intensity I(0) i027224700.00
Molecular weight molecular_weight39558.0 kDa
Excluded volume excluded_volume49524 ų
Envelope volume envelope_volume59153 ų
Hydration-shell volume shell_volume22461 ų
Envelope diameter envelope_diameter77.8
Shell Rg shell_rg28.68
Envelope Rg envelope_rg22.55
Shape Rg shape_rg22.35
Total Rg total_rg23.16
Total atoms total_atoms2763
Residues n_residues370
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 dmax75.6
Rg (real space) rg_real23.10
Rg uncertainty (real space) rg_real_error0.55
I(0) (real space) i0_real2.7220e+07
I(0) uncertainty (real space) i0_real_error3.9250e+05
Rg (reciprocal space) rg_reciprocal23.10
I(0) (reciprocal space) i0_reciprocal27220000.0000
Solution quality estimate total_estimate0.8916
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary24.4
Skewness Skewness skewness0.337
Kurtosis Kurtosis kurtosis-0.481
Angular range angular_range— – 0.3450 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha8610000.0000
Real-space data points n_real_points66
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.879; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.976; Smooth: 0.975

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd1n1l.1
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_idd1n1l.2
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

CATH v4.4 (4 domains)

Domain ID domain_id1n1lA01
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology10 — Thrombin, subunit H
Homologous superfamily homologous superfamily120
Domain ID domain_id1n1lA02
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology10 — Thrombin, subunit H
Homologous superfamily homologous superfamily10 — Trypsin-like serine proteases
Domain ID domain_id1n1lB01
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology10 — Thrombin, subunit H
Homologous superfamily homologous superfamily120
Domain ID domain_id1n1lB02
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)