SAXSdb — 5cq0

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

Capsid protein VP1

Murine polyomavirus (strain P16 small-plaque)

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 × 5 其他Polymer 5 PDB declaration: pentameric（5） Consistent with protein copy count	Chain A； UniProt 34–317 Chain B； UniProt 34–317 Chain C； UniProt 34–317 Chain D； UniProt 34–317 Chain E； UniProt 34–317	Not recorded	;N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose-(1-4)-beta-D-galactopyranose ; × 5 SO4 SULFATE ION × 14 GOL GLYCEROL × 21	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293.15 K；1.5 M ammonium sulfate, 6% (v/v) isopropanol	Resolution 1.90 Å R-free 0.178

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 5CQ0	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1CN3 INTERACTION OF POLYOMAVIRUS INTERNAL PROTEIN VP2 WITH MAJOR CAPSID PROTEIN VP1 AND IMPLICATIONS FOR PARTICIPATION OF VP2 IN VIRAL ENTRY Deposited 1999-05-24	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 34–316（283 aa） Fragment：RESIDUES 35-317 Chain B 34–316（283 aa） Fragment：RESIDUES 35-317 Chain C 34–316（283 aa） Fragment：RESIDUES 35-317 Chain D 34–316（283 aa） Fragment：RESIDUES 35-317 Chain E 34–316（283 aa） Fragment：RESIDUES 35-317	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 4；pH 4.0	Resolution 2.20 Å R-free 0.260
1CN3 INTERACTION OF POLYOMAVIRUS INTERNAL PROTEIN VP2 WITH MAJOR CAPSID PROTEIN VP1 AND IMPLICATIONS FOR PARTICIPATION OF VP2 IN VIRAL ENTRY Deposited 1999-05-24	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric	Chain A 34–316（283 aa） Fragment：RESIDUES 35-317 Chain B 34–316（283 aa） Fragment：RESIDUES 35-317 Chain C 34–316（283 aa） Fragment：RESIDUES 35-317 Chain D 34–316（283 aa） Fragment：RESIDUES 35-317 Chain E 34–316（283 aa） Fragment：RESIDUES 35-317	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 4；pH 4.0	Resolution 2.20 Å R-free 0.260
1SID MURINE POLYOMAVIRUS COMPLEXED WITH 3'SIALYL LACTOSE Deposited 1995-12-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 360 PDB declaration: 360-MERIC	Chain A 1–383（383 aa） Chain B 1–383（383 aa） Chain C 1–383（383 aa） Chain D 1–383（383 aa） Chain E 1–383（383 aa） Chain F 1–383（383 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.65 Å R-free 0.253
1SID MURINE POLYOMAVIRUS COMPLEXED WITH 3'SIALYL LACTOSE Deposited 1995-12-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–383（383 aa） Chain B 1–383（383 aa） Chain C 1–383（383 aa） Chain D 1–383（383 aa） Chain E 1–383（383 aa） Chain F 1–383（383 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.65 Å R-free 0.253
1SID MURINE POLYOMAVIRUS COMPLEXED WITH 3'SIALYL LACTOSE Deposited 1995-12-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Other combination Homooligomer；Protein × 30 PDB declaration: 30-meric	Chain A 1–383（383 aa） Chain B 1–383（383 aa） Chain C 1–383（383 aa） Chain D 1–383（383 aa） Chain E 1–383（383 aa） Chain F 1–383（383 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.65 Å R-free 0.253
1SID MURINE POLYOMAVIRUS COMPLEXED WITH 3'SIALYL LACTOSE Deposited 1995-12-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Other combination Homooligomer；Protein × 36 PDB declaration: 36-meric	Chain A 1–383（383 aa） Chain B 1–383（383 aa） Chain C 1–383（383 aa） Chain D 1–383（383 aa） Chain E 1–383（383 aa） Chain F 1–383（383 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.65 Å R-free 0.253
1SID MURINE POLYOMAVIRUS COMPLEXED WITH 3'SIALYL LACTOSE Deposited 1995-12-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Other combination Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–383（383 aa） Chain B 1–383（383 aa） Chain C 1–383（383 aa） Chain D 1–383（383 aa） Chain E 1–383（383 aa） Chain F 1–383（383 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.65 Å R-free 0.253
1SID MURINE POLYOMAVIRUS COMPLEXED WITH 3'SIALYL LACTOSE Deposited 1995-12-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Other combination Homooligomer；Protein × 30 PDB declaration: 30-meric	Chain A 1–383（383 aa） Chain B 1–383（383 aa） Chain C 1–383（383 aa） Chain D 1–383（383 aa） Chain E 1–383（383 aa） Chain F 1–383（383 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.65 Å R-free 0.253
1SIE MURINE POLYOMAVIRUS COMPLEXED WITH A DISIALYLATED OLIGOSACCHARIDE Deposited 1995-12-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 360 PDB declaration: 360-MERIC	Chain A 1–383（383 aa） Chain B 1–383（383 aa） Chain C 1–383（383 aa） Chain D 1–383（383 aa） Chain E 1–383（383 aa） Chain F 1–383（383 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.65 Å R-free 0.264
1SIE MURINE POLYOMAVIRUS COMPLEXED WITH A DISIALYLATED OLIGOSACCHARIDE Deposited 1995-12-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–383（383 aa） Chain B 1–383（383 aa） Chain C 1–383（383 aa） Chain D 1–383（383 aa） Chain E 1–383（383 aa） Chain F 1–383（383 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.65 Å R-free 0.264
1SIE MURINE POLYOMAVIRUS COMPLEXED WITH A DISIALYLATED OLIGOSACCHARIDE Deposited 1995-12-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Other combination Homooligomer；Protein × 30 PDB declaration: 30-meric	Chain A 1–383（383 aa） Chain B 1–383（383 aa） Chain C 1–383（383 aa） Chain D 1–383（383 aa） Chain E 1–383（383 aa） Chain F 1–383（383 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.65 Å R-free 0.264
1SIE MURINE POLYOMAVIRUS COMPLEXED WITH A DISIALYLATED OLIGOSACCHARIDE Deposited 1995-12-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Other combination Homooligomer；Protein × 36 PDB declaration: 36-meric	Chain A 1–383（383 aa） Chain B 1–383（383 aa） Chain C 1–383（383 aa） Chain D 1–383（383 aa） Chain E 1–383（383 aa） Chain F 1–383（383 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.65 Å R-free 0.264
1SIE MURINE POLYOMAVIRUS COMPLEXED WITH A DISIALYLATED OLIGOSACCHARIDE Deposited 1995-12-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Other combination Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–383（383 aa） Chain B 1–383（383 aa） Chain C 1–383（383 aa） Chain D 1–383（383 aa） Chain E 1–383（383 aa） Chain F 1–383（383 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.65 Å R-free 0.264
1SIE MURINE POLYOMAVIRUS COMPLEXED WITH A DISIALYLATED OLIGOSACCHARIDE Deposited 1995-12-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Other combination Homooligomer；Protein × 30 PDB declaration: 30-meric	Chain A 1–383（383 aa） Chain B 1–383（383 aa） Chain C 1–383（383 aa） Chain D 1–383（383 aa） Chain E 1–383（383 aa） Chain F 1–383（383 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.65 Å R-free 0.264
1VPN UNASSEMBLED POLYOMAVIRUS VP1 PENTAMER Deposited 1997-03-07	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 5 PDB declaration: pentameric	Chain A 32–320（289 aa） Chain B 32–320（289 aa） Chain C 32–320（289 aa） Chain D 32–320（289 aa） Chain E 32–320（289 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；DROP: 1.0 M AMMONIUM PHOSPHATE PH 8.0 2.5 & ETHANOL 8-10 MG/ML PROTEIN RESERVOIR: 2.0 M AMMONIUM PHOSPHATE PH 8.0 5 % ETHANOL	Resolution 2.00 Å R-free 0.199
1VPN UNASSEMBLED POLYOMAVIRUS VP1 PENTAMER Deposited 1997-03-07	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 10 PDB declaration: decameric	Chain A 32–320（289 aa） Chain B 32–320（289 aa） Chain C 32–320（289 aa） Chain D 32–320（289 aa） Chain E 32–320（289 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；DROP: 1.0 M AMMONIUM PHOSPHATE PH 8.0 2.5 & ETHANOL 8-10 MG/ML PROTEIN RESERVOIR: 2.0 M AMMONIUM PHOSPHATE PH 8.0 5 % ETHANOL	Resolution 2.00 Å R-free 0.199
1VPS POLYOMAVIRUS VP1 PENTAMER COMPLEXED WITH A DISIALYLATED HEXASACCHARIDE Deposited 1997-03-07	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 5 PDB declaration: pentameric	Chain A 32–320（289 aa） Chain B 32–320（289 aa） Chain C 32–320（289 aa） Chain D 32–320（289 aa） Chain E 32–320（289 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；DROP: 1.0 M AMMONIUM PHOSPHATE PH 8.0 2.5 & ETHANOL 8-10 MG/ML PROTEIN RESERVOIR: 2.0 M AMMONIUM PHOSPHATE PH 8.0 5 % ETHANOL	Resolution 1.90 Å R-free 0.205
1VPS POLYOMAVIRUS VP1 PENTAMER COMPLEXED WITH A DISIALYLATED HEXASACCHARIDE Deposited 1997-03-07	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Homooligomer；Protein × 10 PDB declaration: decameric	Chain A 32–320（289 aa） Chain B 32–320（289 aa） Chain C 32–320（289 aa） Chain D 32–320（289 aa） Chain E 32–320（289 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；DROP: 1.0 M AMMONIUM PHOSPHATE PH 8.0 2.5 & ETHANOL 8-10 MG/ML PROTEIN RESERVOIR: 2.0 M AMMONIUM PHOSPHATE PH 8.0 5 % ETHANOL	Resolution 1.90 Å R-free 0.205
5CPZ Crystal structure of murine polyomavirus RA strain VP1 in complex with the GT1a glycan Deposited 2015-07-21	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 5 PDB declaration: pentameric	Chain A 34–317（284 aa） Fragment：UNP residues 34-317 Chain B 34–317（284 aa） Fragment：UNP residues 34-317 Chain C 34–317（284 aa） Fragment：UNP residues 34-317 Chain D 34–317（284 aa） Fragment：UNP residues 34-317 Chain E 34–317（284 aa） Fragment：UNP residues 34-317	Not recorded	SO4 SULFATE ION × 14 GOL GLYCEROL × 20	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；1.7 M ammonium sulfate 4.9% (v/v) isopropanol	Resolution 1.71 Å R-free 0.172

6 other PDB entries and 19 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	VP1_POVMP
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–284； UniProt 34–317 Author chain B； PDBConstruct 1–284； UniProt 34–317 Author chain C； PDBConstruct 1–284； UniProt 34–317 Author chain D； PDBConstruct 1–284； UniProt 34–317 Author chain E； PDBConstruct 1–284； UniProt 34–317

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	5cq0
Deposition date deposition_date	2015-07-21
Structure title title	Crystal structure of murine polyomavirus RA strain VP1 in complex with the GD1a glycan
Keywords keywords	Murine Polyomavirus, Virus protein, carbohydrate complex, virus-host interaction, viral protein; VIRAL PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	34.18 Å
Radius of gyration Rg (electron density) rg_electron	33.10 Å
Forward intensity I(0) i0	411276000.00
Molecular weight molecular_weight	161590.0 kDa
Excluded volume excluded_volume	201380 Å³
Envelope volume envelope_volume	252780 Å³
Hydration-shell volume shell_volume	59215 Å³
Envelope diameter envelope_diameter	104.9 Å
Shell Rg shell_rg	42.98 Å
Envelope Rg envelope_rg	32.92 Å
Shape Rg shape_rg	33.02 Å
Total Rg total_rg	34.04 Å
Total atoms total_atoms	11336
Residues n_residues	1400
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	100.4 Å
Rg (real space) rg_real	33.92 Å
Rg uncertainty (real space) rg_real_error	0.44 Å
I(0) (real space) i0_real	4.1130e+08
I(0) uncertainty (real space) i0_real_error	5.1910e+06
Rg (reciprocal space) rg_reciprocal	34.09 Å
I(0) (reciprocal space) i0_reciprocal	411300000.0000
Solution quality estimate total_estimate	0.9013
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	48.0 Å
Skewness Skewness skewness	-0.023
Kurtosis Kurtosis kurtosis	-0.581
Angular range angular_range	— – 0.2300 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	105400000.0000
Real-space data points n_real_points	47
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.941; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.969; Smooth: 0.920

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Capsid protein VP1
Molecular weight formula_weight	31558.7 kDa
Source method src_method	man
Copy count entity_count	5

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E
Atom count atom_count	13481

GMEVLDLVTGPDSVTEIEAFLNPRMGQPPTPESLTEGGQYYGWSRGINLATSDTEDSPGNNTLPTWSMAKLQLPMLNEDLTCDTLQMWEAVSVKTEVVGSGSLLDVHGFNKPTDTVNTKGISTPVEGSQYHVFAVGGEPLDLQGLVTDARTKYKEEGVVTIKTITKKDMVNKDQVLNPISKAKLDKDGMYPVEIWHPDPAKNENTRYFGNYTGGTTTPPVLQFTNTLTTVLLDENGVGPLCKGEGLYLSCVDIMGWRVTRNYDVHHWRGLPRYFKITLRKRWVK

来源 Source

来源生物 organism	Murine polyomavirus (strain P16 small-plaque)
通用名 common_name	MPyV
NCBI Class编号 ncbi_taxonomy_id	47935
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 branched

Description description	;N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose-(1-4)-beta-D-galactopyranose ;
Molecular weight formula_weight	836.7 kDa
Source method src_method	man
Copy count entity_count	5

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	14

Entity 4 Entity 4 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	21

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1793

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7. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (5 domains)

Domain ID domain_id	d5cq0a_
Class class	b — All beta proteins
Fold Fold fold	b.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
Superfamily Superfamily superfamily	b.121.6 — Group I dsDNA viruses
Family Family family	b.121.6.1 — Papovaviridae-like VP

Domain ID domain_id	d5cq0b_
Class class	b — All beta proteins
Fold Fold fold	b.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
Superfamily Superfamily superfamily	b.121.6 — Group I dsDNA viruses
Family Family family	b.121.6.1 — Papovaviridae-like VP

Domain ID domain_id	d5cq0c_
Class class	b — All beta proteins
Fold Fold fold	b.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
Superfamily Superfamily superfamily	b.121.6 — Group I dsDNA viruses
Family Family family	b.121.6.1 — Papovaviridae-like VP

Domain ID domain_id	d5cq0d_
Class class	b — All beta proteins
Fold Fold fold	b.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
Superfamily Superfamily superfamily	b.121.6 — Group I dsDNA viruses
Family Family family	b.121.6.1 — Papovaviridae-like VP

Domain ID domain_id	d5cq0e_
Class class	b — All beta proteins
Fold Fold fold	b.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
Superfamily Superfamily superfamily	b.121.6 — Group I dsDNA viruses
Family Family family	b.121.6.1 — Papovaviridae-like VP

CATH v4.4 (5 domains)

Domain ID domain_id	5cq0A00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	175 — Polyomavirus Vp1; Chain A
Homologous superfamily homologous superfamily	10 — Capsid protein VP1,Polyomavirus

Domain ID domain_id	5cq0B00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	175 — Polyomavirus Vp1; Chain A
Homologous superfamily homologous superfamily	10 — Capsid protein VP1,Polyomavirus

Domain ID domain_id	5cq0C00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	175 — Polyomavirus Vp1; Chain A
Homologous superfamily homologous superfamily	10 — Capsid protein VP1,Polyomavirus

Domain ID domain_id	5cq0D00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	175 — Polyomavirus Vp1; Chain A
Homologous superfamily homologous superfamily	10 — Capsid protein VP1,Polyomavirus

Domain ID domain_id	5cq0E00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	175 — Polyomavirus Vp1; Chain A
Homologous superfamily homologous superfamily	10 — Capsid protein VP1,Polyomavirus

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8. Citations (1)

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Unit-cell length a length_a	219.060 Å
Unit-cell length b length_b	219.060 Å
Unit-cell length c length_c	99.400 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	30

Space group space_group	P 31 2 1
Space-group number int_tables_number	152
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	48.120 Å
R factor r_factor	0.1553
R_work r_work	0.1546
R_free r_free	0.1784

fit	/app/data/saxs_computation/cq/5cq0/5cq0.fit
pddf	/app/data/pr_computation/cq/5cq0/5cq0.pr.out
profile	/app/data/saxs_computation/cq/5cq0/5cq0.dat

Crystal structure of murine polyomavirus RA strain VP1 in complex with the GD1a glycan

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

Capsid protein VP1

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction