5fx6

Novel inhibitors of human rhinovirus 3C protease

Method: X-RAY DIFFRACTION Dmax: 50.9 Å Quality: GOOD

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

RHINOVIRUS 3C PROTEASE

HUMAN RHINOVIRUS 2

UniProt P04936

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 monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain A; UniProt 1508–1687 Fragment:3C PROTEASE, RESIDUES 1508-1687 6OY ethyl (4R)-4-[[(2S,4S)-1-[(2S)-3-methyl-2-[(5-methyl-1,2-oxazol-3-yl)carbonylamino]butanoyl]-4-phenyl-pyrrolidin-2-yl]carbonylamino]-5-[(3S)-2-oxidanylidenepyrrolidin-3-yl]pentanoate × 1 X-RAY DIFFRACTION X-ray crystallization conditions:0.2 M CACL2, 0,1 M TRIS PH 8.5, 25% PEG4000 Resolution 1.45 Å R-free 0.186

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.

17 other PDB entries and 48 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name POLG_HRV2
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 3–182; UniProt 1508–1687

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 5fx6

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5fx6
Download Download

2. Structure Basics 2. Structure Basics

Entry ID entry_id5fx6
Deposition date deposition_date2016-02-24
Structure title titleNovel inhibitors of human rhinovirus 3C protease
Keywords keywordsTRANSFERASE; TRANSFERASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier16.56
Radius of gyration Rg (electron density) rg_electron15.15
Forward intensity I(0) i07774810.00
Molecular weight molecular_weight20568.0 kDa
Excluded volume excluded_volume25854 ų
Envelope volume envelope_volume28574 ų
Hydration-shell volume shell_volume15475 ų
Envelope diameter envelope_diameter50.3
Shell Rg shell_rg21.58
Envelope Rg envelope_rg15.48
Shape Rg shape_rg15.13
Total Rg total_rg16.35
Total atoms total_atoms1449
Residues n_residues180
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 dmax50.9
Rg (real space) rg_real16.41
Rg uncertainty (real space) rg_real_error0.17
I(0) (real space) i0_real7.7750e+06
I(0) uncertainty (real space) i0_real_error7.5650e+04
Rg (reciprocal space) rg_reciprocal16.42
I(0) (reciprocal space) i0_reciprocal7775000.0000
Solution quality estimate total_estimate0.8167
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary22.5
Skewness Skewness skewness0.044
Kurtosis Kurtosis kurtosis-0.457
Angular range angular_range— – 0.4800 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha2684000.0000
Real-space data points n_real_points78
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: 0.975; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd5fx6a_
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.47.1.4 — Viral cysteine protease of trypsin fold

CATH v4.4 (2 domains)

Domain ID domain_id5fx6A01
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology10 — Thrombin, subunit H
Homologous superfamily homologous superfamily10 — Trypsin-like serine proteases
Domain ID domain_id5fx6A02
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)