1sid

MURINE POLYOMAVIRUS COMPLEXED WITH 3'SIALYL LACTOSE

Method: X-RAY DIFFRACTION Dmax: 186.7 Å Quality: GOOD

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

POLYOMAVIRUS COAT PROTEIN VP1

OrganismNot specified

UniProt P49302

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Homooligomer Protein × 360 其他Polymer 360 PDB declaration: 360-MERIC(360) Consistent with protein copy count Chain A; UniProt 1–383 Chain B; UniProt 1–383 Chain C; UniProt 1–383 Chain D; UniProt 1–383 Chain E; UniProt 1–383 Chain F; UniProt 1–383 Not recorded N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose × 360 X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 3.65 Å R-free 0.253
2 Other combination Homooligomer Protein × 6 其他Polymer 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain A; UniProt 1–383 Chain B; UniProt 1–383 Chain C; UniProt 1–383 Chain D; UniProt 1–383 Chain E; UniProt 1–383 Chain F; UniProt 1–383 Not recorded N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose × 6 X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 3.65 Å R-free 0.253
3 Other combination Homooligomer Protein × 30 其他Polymer 30 PDB declaration: 30-meric(30) Consistent with protein copy count Chain A; UniProt 1–383 Chain B; UniProt 1–383 Chain C; UniProt 1–383 Chain D; UniProt 1–383 Chain E; UniProt 1–383 Chain F; UniProt 1–383 Not recorded N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose × 30 X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 3.65 Å R-free 0.253
4 Other combination Homooligomer Protein × 36 其他Polymer 36 PDB declaration: 36-meric(36) Consistent with protein copy count Chain A; UniProt 1–383 Chain B; UniProt 1–383 Chain C; UniProt 1–383 Chain D; UniProt 1–383 Chain E; UniProt 1–383 Chain F; UniProt 1–383 Not recorded N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose × 36 X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 3.65 Å R-free 0.253
5 Other combination Homooligomer Protein × 6 其他Polymer 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain A; UniProt 1–383 Chain B; UniProt 1–383 Chain C; UniProt 1–383 Chain D; UniProt 1–383 Chain E; UniProt 1–383 Chain F; UniProt 1–383 Not recorded N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose × 6 X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 3.65 Å R-free 0.253
6 Other combination Homooligomer Protein × 30 其他Polymer 30 PDB declaration: 30-meric(30) Consistent with protein copy count Chain A; UniProt 1–383 Chain B; UniProt 1–383 Chain C; UniProt 1–383 Chain D; UniProt 1–383 Chain E; UniProt 1–383 Chain F; UniProt 1–383 Not recorded N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose × 30 X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 3.65 Å R-free 0.253

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.

6 other PDB entries and 14 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name COA1_POVMP
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–383; UniProt 1–383 Author chain B; PDBConstruct 1–383; UniProt 1–383 Author chain C; PDBConstruct 1–383; UniProt 1–383 Author chain D; PDBConstruct 1–383; UniProt 1–383 Author chain E; PDBConstruct 1–383; UniProt 1–383 Author chain F; PDBConstruct 1–383; UniProt 1–383

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 1sid

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id1sid
Deposition date deposition_date1995-12-12
Structure title titleMURINE POLYOMAVIRUS COMPLEXED WITH 3'SIALYL LACTOSE
Keywords keywordsCOAT PROTEIN, Icosahedral virus, Virus; VIRUS
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier47.45
Radius of gyration Rg (electron density) rg_electron47.33
Forward intensity I(0) i0865567000.00
Molecular weight molecular_weight242070.0 kDa
Excluded volume excluded_volume302660 ų
Envelope volume envelope_volume475820 ų
Hydration-shell volume shell_volume82411 ų
Envelope diameter envelope_diameter198.7
Shell Rg shell_rg51.34
Envelope Rg envelope_rg49.34
Shape Rg shape_rg47.31
Total Rg total_rg47.58
Total atoms total_atoms17003
Residues n_residues2151
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 dmax186.7
Rg (real space) rg_real47.76
Rg uncertainty (real space) rg_real_error2.62
I(0) (real space) i0_real8.6560e+08
I(0) uncertainty (real space) i0_real_error1.9100e+07
Rg (reciprocal space) rg_reciprocal47.45
I(0) (reciprocal space) i0_reciprocal865200000.0000
Solution quality estimate total_estimate0.7909
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary50.9
Skewness Skewness skewness0.588
Kurtosis Kurtosis kurtosis0.213
Angular range angular_range— – 0.1650 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha60470000.0000
Real-space data points n_real_points34
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.454; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.941; Smooth: 0.974

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (2)

7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_idd1sida_
Class classb — All beta proteins
Fold Fold foldb.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
Superfamily Superfamily superfamilyb.121.6 — Group I dsDNA viruses
Family Family familyb.121.6.1 — Papovaviridae-like VP
Domain ID domain_idd1sidb_
Class classb — All beta proteins
Fold Fold foldb.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
Superfamily Superfamily superfamilyb.121.6 — Group I dsDNA viruses
Family Family familyb.121.6.1 — Papovaviridae-like VP
Domain ID domain_idd1sidc_
Class classb — All beta proteins
Fold Fold foldb.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
Superfamily Superfamily superfamilyb.121.6 — Group I dsDNA viruses
Family Family familyb.121.6.1 — Papovaviridae-like VP
Domain ID domain_idd1sidd_
Class classb — All beta proteins
Fold Fold foldb.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
Superfamily Superfamily superfamilyb.121.6 — Group I dsDNA viruses
Family Family familyb.121.6.1 — Papovaviridae-like VP
Domain ID domain_idd1side_
Class classb — All beta proteins
Fold Fold foldb.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
Superfamily Superfamily superfamilyb.121.6 — Group I dsDNA viruses
Family Family familyb.121.6.1 — Papovaviridae-like VP
Domain ID domain_idd1sidf_
Class classb — All beta proteins
Fold Fold foldb.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
Superfamily Superfamily superfamilyb.121.6 — Group I dsDNA viruses
Family Family familyb.121.6.1 — Papovaviridae-like VP

CATH v4.4 (6 domains)

Domain ID domain_id1sidA00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology175 — Polyomavirus Vp1; Chain A
Homologous superfamily homologous superfamily10 — Capsid protein VP1,Polyomavirus
Domain ID domain_id1sidB00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology175 — Polyomavirus Vp1; Chain A
Homologous superfamily homologous superfamily10 — Capsid protein VP1,Polyomavirus
Domain ID domain_id1sidC00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology175 — Polyomavirus Vp1; Chain A
Homologous superfamily homologous superfamily10 — Capsid protein VP1,Polyomavirus
Domain ID domain_id1sidD00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology175 — Polyomavirus Vp1; Chain A
Homologous superfamily homologous superfamily10 — Capsid protein VP1,Polyomavirus
Domain ID domain_id1sidE00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology175 — Polyomavirus Vp1; Chain A
Homologous superfamily homologous superfamily10 — Capsid protein VP1,Polyomavirus
Domain ID domain_id1sidF00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology175 — Polyomavirus Vp1; Chain A
Homologous superfamily homologous superfamily10 — Capsid protein VP1,Polyomavirus

8. Citations (4)

9. Files and Curves (10)