SAXSdb — 1x9t

▼

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

Penton protein

Human adenovirus 2

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 120	N-terminal peptide of Fiber protein × 60 N-DODECYL-N,N-DIMETHYL-3-AMMONIO-1-PROPANESULFONATE × 120	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	N-terminal peptide of Fiber protein × 1 N-DODECYL-N,N-DIMETHYL-3-AMMONIO-1-PROPANESULFONATE × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 10	N-terminal peptide of Fiber protein × 5 N-DODECYL-N,N-DIMETHYL-3-AMMONIO-1-PROPANESULFONATE × 10	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 12	N-terminal peptide of Fiber protein × 6 N-DODECYL-N,N-DIMETHYL-3-AMMONIO-1-PROPANESULFONATE × 12	Consistent with protein count
5	Protein heterocomplex	Heteromer	Protein 2	N-terminal peptide of Fiber protein × 1 N-DODECYL-N,N-DIMETHYL-3-AMMONIO-1-PROPANESULFONATE × 2	Consistent with protein count
6	Protein heterocomplex	Heteromer	Protein 120	N-terminal peptide of Fiber protein × 60 N-DODECYL-N,N-DIMETHYL-3-AMMONIO-1-PROPANESULFONATE × 120	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PEN3_ADE02
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–523； UniProt 49–571

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	1x9t
Deposition date deposition_date	2004-08-24
Structure title title	The crystal structure of human adenovirus 2 penton base in complex with an ad2 N-terminal fibre peptide
Keywords keywords	jellyroll domain, insertion domain, anti-parallel beta sheets, Virus like Particle-peptide COMPLEX; Virus like Particle/peptide
Experimental Method method	X-RAY DIFFRACTION

▼

3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

1x9t__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

1x9t__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1x9t__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	99.18 Å
Rg (electron density)	98.74 Å
Total Rg	98.82 Å
Atom count	218700
Residues	27000
Excluded volume	3887100 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1x9t__assembly_1__model_1`	complete icosahedral assembly （120）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1x9t__assembly_2__model_1`	dimeric （2）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
3	1	`1x9t__assembly_3__model_1`	decameric （10）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
4	1	`1x9t__assembly_4__model_1`	dodecameric （12）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
5	1	`1x9t__assembly_5__model_1`	dimeric （2）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
6	1	`1x9t__assembly_6__model_1`	120-meric （120）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Penton protein
Molecular weight formula_weight	58218.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	3645

TGGRNSIRYSELAPLFDTTRVYLVDNKSTDVASLNYQNDHSNFLTTVIQNNDYSPGEASTQTINLDDRSHWGGDLKTILHTNMPNVNEFMFTNKFKARVMVSRSLTKDKQVELKYEWVEFTLPEGNYSETMTIDLMNNAIVEHYLKVGRQNGVLESDIGVKFDTRNFRLGFDPVTGLVMPGVYTNEAFHPDIILLPGCGVDFTHSRLSNLLGIRKRQPFQEGFRITYDDLEGGNIPALLDVDAYQASLKDDTEQGGDGAGGGNNSGSGAEENSNAAAAAMQPVEDMNDHAIRGDTFATRAEEKRAEAEAAAEAAAPAAQPEVEKPQKKPVIKPLTEDSKKRSYNLISNDSTFTQYRSWYLAYNYGDPQTGIRSWTLLCTPDVTCGSEQVYWSLPDMMQDPVTFRSTSQISNFPVVGAELLPVHSKSFYNDQAVYSQLIRQFTSLTHVFNRFPENQILARPPAPTITTVSENVPALTDHGTLPLRNSIGGVQRVTITDARRRTCPYVYKALGIVSPRVLSSRTF

Source Source

Source organism organism	Human adenovirus 2
NCBI taxonomy ID ncbi_taxonomy_id	10515
Host organism host_organism	Trichoplusia ni

Entity 2 Entity 2 polymer

Description description	N-terminal peptide of Fiber protein
Molecular weight formula_weight	2522.8 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MKRARPSEDTFNPVYPYDTEC

Entity 3 Entity 3 non-polymer

Description description	N-DODECYL-N,N-DIMETHYL-3-AMMONIO-1-PROPANESULFONATE
Molecular weight formula_weight	336.6 kDa
Source method src_method	syn
Copy count entity_count	2

▼

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	1x9tA01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	550 — Penton protein; domain 1

Domain ID domain_id	1x9tA02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1620 — adenovirus 2 penton base, domain 2
Homologous superfamily homologous superfamily	10 — adenovirus 2 penton base, domain 2

▶

Unit-cell length a length_a	438.370 Å
Unit-cell length b length_b	299.825 Å
Unit-cell length c length_c	419.583 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	103.22 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	240

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

Resolution resolution	3.500 Å
Low-resolution limit resolution_low	29.980 Å
R factor r_factor	0.3060
R_work r_work	0.3060
R_free r_free	0.3030

The crystal structure of human adenovirus 2 penton base in complex with an ad2 N-terminal fibre peptide

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

Penton protein

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

1x9t__assembly_1__model_1

1x9t__assembly_1__model_1 | I(q)

1x9t__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

The crystal structure of human adenovirus 2 penton base in complex with an ad2 N-terminal fibre peptide

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

Penton protein

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

1x9t__assembly_1__model_1

1x9t__assembly_1__model_1 | I(q)

1x9t__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)