SAXSdb — 1nob

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

PROTEIN (FIBER KNOB PROTEIN)

Human adenovirus 12

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 × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 403–587 Chain B； UniProt 403–587 Chain C； UniProt 403–587	Fragment：KNOB	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7；26% PEG 3350, pH 7.0	Resolution 2.60 Å R-free 0.290
2	Protein homooligomer Homooligomer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain D； UniProt 403–587 Chain E； UniProt 403–587 Chain F； UniProt 403–587	Fragment：KNOB	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7；26% PEG 3350, pH 7.0	Resolution 2.60 Å R-free 0.290

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 1NOB	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1KAC KNOB DOMAIN FROM ADENOVIRUS SEROTYPE 12 IN COMPLEX WITH DOMAIN 1 OF ITS CELLULAR RECEPTOR CAR Deposited 1999-05-05	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 403–587（185 aa） Fragment：KNOB	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.2；900MM AMMONIUM SULPHATE ON 100MM MES, PH 6.2	Resolution 2.60 Å R-free 0.250
1P69 STRUCTURAL BASIS FOR VARIATION IN ADENOVIRUS AFFINITY FOR THE CELLULAR RECEPTOR CAR (P417S MUTANT) Deposited 2003-04-29	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 403–587（185 aa）	Mutation：P417S	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；VAPOR DIFFUSION, SITTING DROP	Resolution 3.10 Å R-free 0.256
1P6A STRUCTURAL BASIS FOR VARIATION IN ADENOVIRUS AFFINITY FOR THE CELLULAR RECEPTOR CAR (S489Y MUTANT) Deposited 2003-04-29	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 403–587（185 aa） Fragment：knob domain (UNP residues 403-587)	Mutation：Y489S	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP	Resolution 2.90 Å R-free 0.252

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

View Construct and Data Evidence

UniProt name	FIBP_ADE12
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–185； UniProt 403–587 Author chain B； PDBConstruct 1–185； UniProt 403–587 Author chain C； PDBConstruct 1–185； UniProt 403–587 Author chain D； PDBConstruct 1–185； UniProt 403–587 Author chain E； PDBConstruct 1–185； UniProt 403–587 Author chain F； PDBConstruct 1–185； UniProt 403–587

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	1nob
Deposition date deposition_date	1999-05-05
Structure title title	KNOB DOMAIN FROM ADENOVIRUS SEROTYPE 12
Keywords keywords	RECEPTOR BINDING, 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	36.65 Å
Radius of gyration Rg (electron density) rg_electron	36.41 Å
Forward intensity I(0) i0	212911000.00
Molecular weight molecular_weight	119610.0 kDa
Excluded volume excluded_volume	150200 Å³
Envelope volume envelope_volume	183920 Å³
Hydration-shell volume shell_volume	42604 Å³
Envelope diameter envelope_diameter	124.2 Å
Shell Rg shell_rg	41.95 Å
Envelope Rg envelope_rg	36.09 Å
Shape Rg shape_rg	36.41 Å
Total Rg total_rg	36.79 Å
Total atoms total_atoms	8406
Residues n_residues	1110
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	117.2 Å
Rg (real space) rg_real	36.83 Å
Rg uncertainty (real space) rg_real_error	0.83 Å
I(0) (real space) i0_real	2.1290e+08
I(0) uncertainty (real space) i0_real_error	3.2870e+06
Rg (reciprocal space) rg_reciprocal	36.72 Å
I(0) (reciprocal space) i0_reciprocal	212900000.0000
Solution quality estimate total_estimate	0.6308
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	32.7 Å
Skewness Skewness skewness	0.401
Kurtosis Kurtosis kurtosis	-0.616
Angular range angular_range	— – 0.2150 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	63120000.0000
Real-space data points n_real_points	44
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.830; Stabil: 1.000; Sysdev: 0.048; Positv: 1.000; Valcen: 0.892; Smooth: 0.670

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d1noba_
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	d1nobb_
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	d1nobc_
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	d1nobd_
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	d1nobe_
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	d1nobf_
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	1nobA00
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	1nobB00
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	1nobC00
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	1nobD00
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	1nobE00
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	1nobF00
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	61.910 Å
Unit-cell length b length_b	104.820 Å
Unit-cell length c length_c	77.190 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	96.90 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.600 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	—
R_work r_work	0.2400
R_free r_free	0.2900

Description description	PROTEIN (FIBER KNOB PROTEIN)
Molecular weight formula_weight	19944.5 kDa
Source method src_method	man
Copy count entity_count	6

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	8406

KNOB DOMAIN FROM ADENOVIRUS SEROTYPE 12

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

PROTEIN (FIBER KNOB 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

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Human adenovirus 12
NCBI Class编号 ncbi_taxonomy_id	28282
宿主生物 host_organism	Escherichia coli

fit	/app/data/saxs_computation/no/1nob/1nob.fit
pddf	/app/data/pr_computation/no/1nob/1nob.pr.out
profile	/app/data/saxs_computation/no/1nob/1nob.dat