7ara

Rhinovirus A2 2A protease in complex with zVAM.fmk

Method: X-RAY DIFFRACTION Dmax: 69.7 Å Quality: GOOD

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

2A 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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 851–992 Chain B; UniProt 851–992 Not recorded S7N (phenylmethyl) ~{N}-[(2~{R})-3-methyl-1-[[(2~{S})-1-[[(3~{S})-1-methylsulfanyl-4-oxidanylidene-pentan-3-yl]amino]-1-oxidanylidene-propan-2-yl]amino]-1-oxidanylidene-butan-2-yl]carbamate × 1 ZN ZINC ION × 2 S7Q (phenylmethyl) ~{N}-[(2~{S})-3-methyl-1-[[(2~{R})-1-[[(3~{R})-1-methylsulfanyl-4-oxidanylidene-pentan-3-yl]amino]-1-oxidanylidene-propan-2-yl]amino]-1-oxidanylidene-butan-2-yl]carbamate × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;277.15 K;7.5 % PEG8000, 0.3 M KCNS, 5 % 2-methyl-2-butanol, 10 % glycerol, 10 mM b-mercaptoethanol and 50 mM sodium-potassium phosphate buffer pH 8.0 Resolution 2.24 Å R-free 0.257

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 1–142; UniProt 851–992 Author chain B; PDBConstruct 1–142; UniProt 851–992

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 7ara

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7ara
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2. Structure Basics 2. Structure Basics

Entry ID entry_id7ara
Deposition date deposition_date2020-10-23
Structure title titleRhinovirus A2 2A protease in complex with zVAM.fmk
Keywords keywordsChymotrypsin-like cysteine protease, rhinoviral 2A protease, zVAM.fmk, VIRAL PROTEIN; VIRAL PROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier21.28
Radius of gyration Rg (electron density) rg_electron20.60
Forward intensity I(0) i018694500.00
Molecular weight molecular_weight31989.0 kDa
Excluded volume excluded_volume39567 ų
Envelope volume envelope_volume47141 ų
Hydration-shell volume shell_volume19611 ų
Envelope diameter envelope_diameter70.3
Shell Rg shell_rg26.68
Envelope Rg envelope_rg21.04
Shape Rg shape_rg20.65
Total Rg total_rg21.27
Total atoms total_atoms2243
Residues n_residues278
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 dmax69.7
Rg (real space) rg_real21.31
Rg uncertainty (real space) rg_real_error0.42
I(0) (real space) i0_real1.8690e+07
I(0) uncertainty (real space) i0_real_error2.2890e+05
Rg (reciprocal space) rg_reciprocal21.31
I(0) (reciprocal space) i0_reciprocal18690000.0000
Solution quality estimate total_estimate0.8851
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary22.5
Skewness Skewness skewness0.398
Kurtosis Kurtosis kurtosis-0.351
Angular range angular_range— – 0.3750 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha5577000.0000
Real-space data points n_real_points69
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.848; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.976; Smooth: 0.981

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd7araa_
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.47.1.0 — automated matches
Domain ID domain_idd7arab_
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.47.1.0 — automated matches

8. Citations (1)

9. Files and Curves (10)