SAXSdb — 2wbv

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

FIBER PROTEIN

CANINE ADENOVIRUS 2

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 × 3 其他Polymer 1 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 358–542 Chain B； UniProt 358–542 Chain D； UniProt 358–542	Fragment：FIBRE HEAD, RESIDUES 358-542	N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose × 1 GOL GLYCEROL × 3 SIA N-acetyl-alpha-neuraminic acid × 2	X-RAY DIFFRACTION X-ray crystallization conditions：5% PEG 4000, 5% ISOPROPANOL, 0.1 M HEPES PH 7.4	Resolution 1.90 Å R-free 0.195
2	Protein homooligomer Homooligomer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain C； UniProt 358–542 Chain E； UniProt 358–542 Chain F； UniProt 358–542	Fragment：FIBRE HEAD, RESIDUES 358-542	GOL GLYCEROL × 3 SIA N-acetyl-alpha-neuraminic acid × 3	X-RAY DIFFRACTION X-ray crystallization conditions：5% PEG 4000, 5% ISOPROPANOL, 0.1 M HEPES PH 7.4	Resolution 1.90 Å R-free 0.195

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 2WBV	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2J1K CAV-2 fibre head in complex with CAR D1 Deposited 2006-08-14	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 C 358–542（185 aa） Fragment：FIBRE HEAD DOMAIN, RESIDUES 358-542 Chain H 358–542（185 aa） Fragment：FIBRE HEAD DOMAIN, RESIDUES 358-542 Chain I 358–542（185 aa） Fragment：FIBRE HEAD DOMAIN, RESIDUES 358-542	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.30 Å R-free 0.220
2J1K CAV-2 fibre head in complex with CAR D1 Deposited 2006-08-14	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain D 358–542（185 aa） Fragment：FIBRE HEAD DOMAIN, RESIDUES 358-542 Chain E 358–542（185 aa） Fragment：FIBRE HEAD DOMAIN, RESIDUES 358-542 Chain F 358–542（185 aa） Fragment：FIBRE HEAD DOMAIN, RESIDUES 358-542	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.30 Å R-free 0.220
2J1K CAV-2 fibre head in complex with CAR D1 Deposited 2006-08-14	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain L 358–542（185 aa） Fragment：FIBRE HEAD DOMAIN, RESIDUES 358-542 Chain M 358–542（185 aa） Fragment：FIBRE HEAD DOMAIN, RESIDUES 358-542 Chain N 358–542（185 aa） Fragment：FIBRE HEAD DOMAIN, RESIDUES 358-542	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.30 Å R-free 0.220
2J1K CAV-2 fibre head in complex with CAR D1 Deposited 2006-08-14	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain Q 358–542（185 aa） Fragment：FIBRE HEAD DOMAIN, RESIDUES 358-542 Chain R 358–542（185 aa） Fragment：FIBRE HEAD DOMAIN, RESIDUES 358-542 Chain S 358–542（185 aa） Fragment：FIBRE HEAD DOMAIN, RESIDUES 358-542	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.30 Å R-free 0.220
2J2J Canine adenovirus fibre head at 1.5 A resolution Deposited 2006-08-16	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 358–542（185 aa） Fragment：FIBRE HEAD DOMAIN, RESIDUES 358-542 Chain B 358–542（185 aa） Fragment：FIBRE HEAD DOMAIN, RESIDUES 358-542 Chain D 358–542（185 aa） Fragment：FIBRE HEAD DOMAIN, RESIDUES 358-542	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions 0.15 M KBR, 30% PEG MONOMETHYL-ETHER 2000	Resolution 1.50 Å R-free 0.206
2J2J Canine adenovirus fibre head at 1.5 A resolution Deposited 2006-08-16	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain C 358–542（185 aa） Fragment：FIBRE HEAD DOMAIN, RESIDUES 358-542 Chain E 358–542（185 aa） Fragment：FIBRE HEAD DOMAIN, RESIDUES 358-542 Chain F 358–542（185 aa） Fragment：FIBRE HEAD DOMAIN, RESIDUES 358-542	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions 0.15 M KBR, 30% PEG MONOMETHYL-ETHER 2000	Resolution 1.50 Å R-free 0.206
2W9L CANINE ADENOVIRUS TYPE 2 FIBRE HEAD IN COMPLEX WITH CAR DOMAIN D1 AND SIALIC ACID Deposited 2009-01-26	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric	Chain Q 358–542（185 aa） Fragment：FIBRE HEAD, RESIDUES 358-542 Chain R 358–542（185 aa） Fragment：FIBRE HEAD, RESIDUES 358-542 Chain S 358–542（185 aa） Fragment：FIBRE HEAD, RESIDUES 358-542	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions 20% POLYETHYLENE GLYCOL MONOMETHYL-ETHER 550, 0.1 M BICINE, PH 9, 0.1 M NACL	Resolution 2.91 Å R-free 0.254
2W9L CANINE ADENOVIRUS TYPE 2 FIBRE HEAD IN COMPLEX WITH CAR DOMAIN D1 AND SIALIC ACID Deposited 2009-01-26	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Heteromer；Protein × 6 PDB declaration: hexameric	Chain D 358–542（185 aa） Fragment：FIBRE HEAD, RESIDUES 358-542 Chain E 358–542（185 aa） Fragment：FIBRE HEAD, RESIDUES 358-542 Chain F 358–542（185 aa） Fragment：FIBRE HEAD, RESIDUES 358-542	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions 20% POLYETHYLENE GLYCOL MONOMETHYL-ETHER 550, 0.1 M BICINE, PH 9, 0.1 M NACL	Resolution 2.91 Å R-free 0.254
2W9L CANINE ADENOVIRUS TYPE 2 FIBRE HEAD IN COMPLEX WITH CAR DOMAIN D1 AND SIALIC ACID Deposited 2009-01-26	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Other combination Heteromer；Protein × 6 PDB declaration: hexameric	Chain C 358–542（185 aa） Fragment：FIBRE HEAD, RESIDUES 358-542 Chain H 358–542（185 aa） Fragment：FIBRE HEAD, RESIDUES 358-542 Chain I 358–542（185 aa） Fragment：FIBRE HEAD, RESIDUES 358-542	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions 20% POLYETHYLENE GLYCOL MONOMETHYL-ETHER 550, 0.1 M BICINE, PH 9, 0.1 M NACL	Resolution 2.91 Å R-free 0.254
2W9L CANINE ADENOVIRUS TYPE 2 FIBRE HEAD IN COMPLEX WITH CAR DOMAIN D1 AND SIALIC ACID Deposited 2009-01-26	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Other combination Heteromer；Protein × 6 PDB declaration: hexameric	Chain L 358–542（185 aa） Fragment：FIBRE HEAD, RESIDUES 358-542 Chain M 358–542（185 aa） Fragment：FIBRE HEAD, RESIDUES 358-542 Chain N 358–542（185 aa） Fragment：FIBRE HEAD, RESIDUES 358-542	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions 20% POLYETHYLENE GLYCOL MONOMETHYL-ETHER 550, 0.1 M BICINE, PH 9, 0.1 M NACL	Resolution 2.91 Å R-free 0.254

3 other PDB entries and 10 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	FIBP_ADECT
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–189； UniProt 358–542 Author chain B； PDBConstruct 5–189； UniProt 358–542 Author chain C； PDBConstruct 5–189； UniProt 358–542 Author chain D； PDBConstruct 5–189； UniProt 358–542 Author chain E； PDBConstruct 5–189； UniProt 358–542 Author chain F； PDBConstruct 5–189； UniProt 358–542

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	2wbv
Deposition date deposition_date	2009-03-05
Structure title title	Canine adenovirus 2 fibre head in complex with sialic acid
Keywords keywords	;KNOB, HEAD, FIBER, VIRUS, FIBRE, ADENOVIRUS, HEMAGGLUTINATION, STRUCTURAL PROTEIN, RED BLOOD CELL, SIALYL-LACTOSE, CELL ATTACHMENT, ERYTHROCYTE, SIALIC ACID, FIBER PROTEIN ;; STRUCTURAL 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	34.79 Å
Radius of gyration Rg (electron density) rg_electron	34.40 Å
Forward intensity I(0) i0	235209000.00
Molecular weight molecular_weight	123440.0 kDa
Excluded volume excluded_volume	154280 Å³
Envelope volume envelope_volume	184420 Å³
Hydration-shell volume shell_volume	44899 Å³
Envelope diameter envelope_diameter	120.7 Å
Shell Rg shell_rg	40.65 Å
Envelope Rg envelope_rg	34.10 Å
Shape Rg shape_rg	34.42 Å
Total Rg total_rg	34.78 Å
Total atoms total_atoms	8665
Residues n_residues	1101
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	111.2 Å
Rg (real space) rg_real	34.91 Å
Rg uncertainty (real space) rg_real_error	0.77 Å
I(0) (real space) i0_real	2.3520e+08
I(0) uncertainty (real space) i0_real_error	3.5570e+06
Rg (reciprocal space) rg_reciprocal	34.84 Å
I(0) (reciprocal space) i0_reciprocal	235200000.0000
Solution quality estimate total_estimate	0.8593
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	34.6 Å
Skewness Skewness skewness	0.443
Kurtosis Kurtosis kurtosis	-0.425
Angular range angular_range	— – 0.2250 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	61080000.0000
Real-space data points n_real_points	46
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.843; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.985; Smooth: 0.654

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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	FIBER PROTEIN
Molecular weight formula_weight	20626.4 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	9900

GAMSPPAAPITLWTGPGPSINGFINDTPVIRCFICLTRDSNLVTVNASFVGEGGYRIVSPTQSQFSLIMEFDQFGQLMSTGNINSTTTWGEKPWGNNTVQPRPSHTWKLCMPNREVYSTPAATISRCGLDSIAVDGAPSRSIDCMLIINKPKGVATYTLTFRFLNFNRLSGGTLFKTDVLTFTYVGENQ

来源 Source

来源生物 organism	CANINE ADENOVIRUS 2
NCBI Class编号 ncbi_taxonomy_id	10514
宿主生物 host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 branched

Description description	N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose
Molecular weight formula_weight	471.4 kDa
Source method src_method	man
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 4 Entity 4 non-polymer

Description description	N-acetyl-alpha-neuraminic acid
Molecular weight formula_weight	309.3 kDa
Source method src_method	man
Copy count entity_count	5

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1152

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7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d2wbva_
Class class	b — All beta proteins
Fold Fold fold	b.21 — Virus attachment protein globular domain
Superfamily Superfamily superfamily	b.21.1 — Virus attachment protein globular domain
Family Family family	b.21.1.1 — Adenovirus fiber protein 'knob' domain

Domain ID domain_id	d2wbvb_
Class class	b — All beta proteins
Fold Fold fold	b.21 — Virus attachment protein globular domain
Superfamily Superfamily superfamily	b.21.1 — Virus attachment protein globular domain
Family Family family	b.21.1.1 — Adenovirus fiber protein 'knob' domain

Domain ID domain_id	d2wbvc_
Class class	b — All beta proteins
Fold Fold fold	b.21 — Virus attachment protein globular domain
Superfamily Superfamily superfamily	b.21.1 — Virus attachment protein globular domain
Family Family family	b.21.1.1 — Adenovirus fiber protein 'knob' domain

Domain ID domain_id	d2wbvd_
Class class	b — All beta proteins
Fold Fold fold	b.21 — Virus attachment protein globular domain
Superfamily Superfamily superfamily	b.21.1 — Virus attachment protein globular domain
Family Family family	b.21.1.1 — Adenovirus fiber protein 'knob' domain

Domain ID domain_id	d2wbve_
Class class	b — All beta proteins
Fold Fold fold	b.21 — Virus attachment protein globular domain
Superfamily Superfamily superfamily	b.21.1 — Virus attachment protein globular domain
Family Family family	b.21.1.1 — Adenovirus fiber protein 'knob' domain

Domain ID domain_id	d2wbvf_
Class class	b — All beta proteins
Fold Fold fold	b.21 — Virus attachment protein globular domain
Superfamily Superfamily superfamily	b.21.1 — Virus attachment protein globular domain
Family Family family	b.21.1.1 — Adenovirus fiber protein 'knob' domain

CATH v4.4 (6 domains)

Domain ID domain_id	2wbvA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	90 — Adenovirus Type 5 Fiber Protein (Receptor Binding Domain)
Homologous superfamily homologous superfamily	10 — Adenovirus pIV-related, attachment domain

Domain ID domain_id	2wbvB00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	90 — Adenovirus Type 5 Fiber Protein (Receptor Binding Domain)
Homologous superfamily homologous superfamily	10 — Adenovirus pIV-related, attachment domain

Domain ID domain_id	2wbvC00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	90 — Adenovirus Type 5 Fiber Protein (Receptor Binding Domain)
Homologous superfamily homologous superfamily	10 — Adenovirus pIV-related, attachment domain

Domain ID domain_id	2wbvD00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	90 — Adenovirus Type 5 Fiber Protein (Receptor Binding Domain)
Homologous superfamily homologous superfamily	10 — Adenovirus pIV-related, attachment domain

Domain ID domain_id	2wbvE00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	90 — Adenovirus Type 5 Fiber Protein (Receptor Binding Domain)
Homologous superfamily homologous superfamily	10 — Adenovirus pIV-related, attachment domain

Domain ID domain_id	2wbvF00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	90 — Adenovirus Type 5 Fiber Protein (Receptor Binding Domain)
Homologous superfamily homologous superfamily	10 — Adenovirus pIV-related, attachment domain

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8. Citations (1)

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Unit-cell length a length_a	215.000 Å
Unit-cell length b length_b	61.250 Å
Unit-cell length c length_c	143.110 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	131.67 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	24

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	46.130 Å
R factor r_factor	0.1590
R_work r_work	0.1570
R_free r_free	0.1950

fit	/app/data/saxs_computation/wb/2wbv/2wbv.fit
pddf	/app/data/pr_computation/wb/2wbv/2wbv.pr.out
profile	/app/data/saxs_computation/wb/2wbv/2wbv.dat

Canine adenovirus 2 fibre head in complex with sialic acid

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

FIBER PROTEIN

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