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1ijs

CPV (STRAIN D) mutant A300D, complex (VIRAL COAT/DNA), VP2, PH=7.5, T=4 DEGREES C

Method: X-RAY DIFFRACTION Dmax: 105.7 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

PROTEIN (PARVOVIRUS COAT PROTEIN)

Canine parvovirus

UniProt P30129

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–DNA Homooligomer Protein × 60 DNA 120 PDB declaration: 180-MERIC（180） Consistent with all polymer counts Chain P； UniProt 1–584 Mutation：A300D ;DNA (5'-D(*CP*CP*AP*CP*CP*CP*CP*AP*A)-3') ; × 60 ;DNA (5'-D(*AP*C)-3') ; × 60 X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.5；0.75% PEG8000, 10MM TRIS-HCL, 8MM CACL2.2H2O, PH=7.5 Resolution 3.25 Å
2 Protein–DNA Monomer Protein × 1 DNA 2 PDB declaration: trimeric（3） Consistent with all polymer counts Chain P； UniProt 1–584 Mutation：A300D ;DNA (5'-D(*CP*CP*AP*CP*CP*CP*CP*AP*A)-3') ; × 1 ;DNA (5'-D(*AP*C)-3') ; × 1 X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.5；0.75% PEG8000, 10MM TRIS-HCL, 8MM CACL2.2H2O, PH=7.5 Resolution 3.25 Å
3 Protein–DNA Homooligomer Protein × 5 DNA 10 PDB declaration: pentadecameric（15） Consistent with all polymer counts Chain P； UniProt 1–584 Mutation：A300D ;DNA (5'-D(*CP*CP*AP*CP*CP*CP*CP*AP*A)-3') ; × 5 ;DNA (5'-D(*AP*C)-3') ; × 5 X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.5；0.75% PEG8000, 10MM TRIS-HCL, 8MM CACL2.2H2O, PH=7.5 Resolution 3.25 Å
4 Protein–DNA Homooligomer Protein × 6 DNA 12 PDB declaration: octadecameric（18） Consistent with all polymer counts Chain P； UniProt 1–584 Mutation：A300D ;DNA (5'-D(*CP*CP*AP*CP*CP*CP*CP*AP*A)-3') ; × 6 ;DNA (5'-D(*AP*C)-3') ; × 6 X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.5；0.75% PEG8000, 10MM TRIS-HCL, 8MM CACL2.2H2O, PH=7.5 Resolution 3.25 Å
5 Protein–DNA Monomer Protein × 1 DNA 2 PDB declaration: trimeric（3） Consistent with all polymer counts Chain P； UniProt 1–584 Mutation：A300D ;DNA (5'-D(*CP*CP*AP*CP*CP*CP*CP*AP*A)-3') ; × 1 ;DNA (5'-D(*AP*C)-3') ; × 1 X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.5；0.75% PEG8000, 10MM TRIS-HCL, 8MM CACL2.2H2O, PH=7.5 Resolution 3.25 Å
6 Protein–DNA Homooligomer Protein × 60 DNA 120 PDB declaration: 180-meric（180） Consistent with all polymer counts Chain P； UniProt 1–584 Mutation：A300D ;DNA (5'-D(*CP*CP*AP*CP*CP*CP*CP*AP*A)-3') ; × 60 ;DNA (5'-D(*AP*C)-3') ; × 60 X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.5；0.75% PEG8000, 10MM TRIS-HCL, 8MM CACL2.2H2O, PH=7.5 Resolution 3.25 Å

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.

Other PDB Difference from Current Entry 1IJS Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1C8D CANINE PANLEUKOPENIA VIRUS EMPTY CAPSID STRUCTURE Deposited 2000-05-05 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 60 PDB declaration: complete icosahedral assembly
Chain A 1–584（584 aa）
Not recorded CA CALCIUM ION × 60 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；0.75-1.5% PEG8000, 20 mM TRIS pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Resolution 3.00 Å
1C8D CANINE PANLEUKOPENIA VIRUS EMPTY CAPSID STRUCTURE Deposited 2000-05-05 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–584（584 aa）
Not recorded CA CALCIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；0.75-1.5% PEG8000, 20 mM TRIS pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Resolution 3.00 Å
1C8D CANINE PANLEUKOPENIA VIRUS EMPTY CAPSID STRUCTURE Deposited 2000-05-05 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 5 PDB declaration: pentameric
Chain A 1–584（584 aa）
Not recorded CA CALCIUM ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；0.75-1.5% PEG8000, 20 mM TRIS pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Resolution 3.00 Å
1C8D CANINE PANLEUKOPENIA VIRUS EMPTY CAPSID STRUCTURE Deposited 2000-05-05 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 1–584（584 aa）
Not recorded CA CALCIUM ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；0.75-1.5% PEG8000, 20 mM TRIS pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Resolution 3.00 Å
1C8D CANINE PANLEUKOPENIA VIRUS EMPTY CAPSID STRUCTURE Deposited 2000-05-05 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–584（584 aa）
Not recorded CA CALCIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；0.75-1.5% PEG8000, 20 mM TRIS pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Resolution 3.00 Å
1C8D CANINE PANLEUKOPENIA VIRUS EMPTY CAPSID STRUCTURE Deposited 2000-05-05 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 6 Protein homooligomer Homooligomer；Protein × 60 PDB declaration: 60-meric
Chain A 1–584（584 aa）
Not recorded CA CALCIUM ION × 60 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；0.75-1.5% PEG8000, 20 mM TRIS pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Resolution 3.00 Å
1P5Y The structures of host range controlling regions of the capsids of canine and feline parvoviruses and mutants Deposited 2003-04-28 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 60 PDB declaration: complete icosahedral assembly
Chain A 37–584（548 aa） Fragment：SEQUENCE DATABASE RESIDUES 190-737
Mutation：N93D No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；PEG8000, CaCl2, Tris.HCL, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 3.20 Å R-free 0.253
1P5Y The structures of host range controlling regions of the capsids of canine and feline parvoviruses and mutants Deposited 2003-04-28 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 37–584（548 aa） Fragment：SEQUENCE DATABASE RESIDUES 190-737
Mutation：N93D No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；PEG8000, CaCl2, Tris.HCL, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 3.20 Å R-free 0.253
1P5Y The structures of host range controlling regions of the capsids of canine and feline parvoviruses and mutants Deposited 2003-04-28 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 5 PDB declaration: pentameric
Chain A 37–584（548 aa） Fragment：SEQUENCE DATABASE RESIDUES 190-737
Mutation：N93D No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；PEG8000, CaCl2, Tris.HCL, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 3.20 Å R-free 0.253
1P5Y The structures of host range controlling regions of the capsids of canine and feline parvoviruses and mutants Deposited 2003-04-28 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 4 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 37–584（548 aa） Fragment：SEQUENCE DATABASE RESIDUES 190-737
Mutation：N93D No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；PEG8000, CaCl2, Tris.HCL, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 3.20 Å R-free 0.253
1P5Y The structures of host range controlling regions of the capsids of canine and feline parvoviruses and mutants Deposited 2003-04-28 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 37–584（548 aa） Fragment：SEQUENCE DATABASE RESIDUES 190-737
Mutation：N93D No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；PEG8000, CaCl2, Tris.HCL, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 3.20 Å R-free 0.253
1P5Y The structures of host range controlling regions of the capsids of canine and feline parvoviruses and mutants Deposited 2003-04-28 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 6 Protein homooligomer Homooligomer；Protein × 60 PDB declaration: 60-meric
Chain A 37–584（548 aa） Fragment：SEQUENCE DATABASE RESIDUES 190-737
Mutation：N93D No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；PEG8000, CaCl2, Tris.HCL, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 3.20 Å R-free 0.253

2 other PDB entries and 12 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name COAT_PAVC2
Isoform —
PDB entities 3
Chains and sequence ranges Author chain P； PDBConstruct 1–584； UniProt 1–584

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 1ijs

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id1ijs
Deposition date deposition_date1996-09-12
Structure title titleCPV (STRAIN D) mutant A300D, complex (VIRAL COAT/DNA), VP2, PH=7.5, T=4 DEGREES C
Keywords keywordsMUTANT A300D, VIRAL COAT PROTEIN, COMPLEX (PARVOVIRUS COAT PROTEIN-DNA), Icosahedral virus, Virus-DNA COMPLEX; Virus/DNA
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier30.20 Å
Radius of gyration Rg (electron density) rg_electron29.15 Å
Forward intensity I(0) i075172400.00
Molecular weight molecular_weight64884.0 kDa
Excluded volume excluded_volume79820 ų
Envelope volume envelope_volume115600 ų
Hydration-shell volume shell_volume33891 ų
Envelope diameter envelope_diameter109.6 Å
Shell Rg shell_rg35.20 Å
Envelope Rg envelope_rg29.76 Å
Shape Rg shape_rg29.09 Å
Total Rg total_rg29.92 Å
Total atoms total_atoms4571
Residues n_residues559
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−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
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax105.7 Å
Rg (real space) rg_real30.25 Å
Rg uncertainty (real space) rg_real_error0.91 Å
I(0) (real space) i0_real7.5170e+07
I(0) uncertainty (real space) i0_real_error1.2670e+06
Rg (reciprocal space) rg_reciprocal30.23 Å
I(0) (reciprocal space) i0_reciprocal75170000.0000
Solution quality estimate total_estimate0.6497
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary34.6 Å
Skewness Skewness skewness0.435
Kurtosis Kurtosis kurtosis-0.105
Angular range angular_range— – 0.2600 Å−1
Current regularization parameter α current_alpha0.0001
Highest regularization parameter α highest_alpha7190000.0000
Real-space data points n_real_points53
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.763; Stabil: 1.000; Sysdev: 0.077; Positv: 1.000; Valcen: 0.965; Smooth: 0.957
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1ijsp_
Class classb — All beta proteins
Fold Fold foldb.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
Superfamily Superfamily superfamilyb.121.5 — ssDNA viruses
Family Family familyb.121.5.2 — Parvoviridae-like VP

CATH v4.4 (1 domains)

Domain ID domain_id1ijsP00
Class class2 — Mainly Beta
Architecture architecture170 — Beta Complex
Topology topology30 — Empty Capsid Viral Protein 2
Homologous superfamily homologous superfamily10 — Parvovirus coat protein VP1/VP2
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8. Citations (5)

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9. Files and Curves (10)