SAXSdb — 1x9p

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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 homooligomer	Homooligomer	Protein 60	SULFATE ION × 60 N-DODECYL-N,N-DIMETHYL-3-AMMONIO-1-PROPANESULFONATE × 120	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	SULFATE ION × 1 N-DODECYL-N,N-DIMETHYL-3-AMMONIO-1-PROPANESULFONATE × 2	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 5	SULFATE ION × 5 N-DODECYL-N,N-DIMETHYL-3-AMMONIO-1-PROPANESULFONATE × 10	Consistent with protein count
4	Protein homooligomer	Homooligomer	Protein 6	SULFATE ION × 6 N-DODECYL-N,N-DIMETHYL-3-AMMONIO-1-PROPANESULFONATE × 12	Consistent with protein count
5	Protein monomer	Monomer	Protein 1	SULFATE ION × 1 N-DODECYL-N,N-DIMETHYL-3-AMMONIO-1-PROPANESULFONATE × 2	Consistent with protein count
6	Protein homooligomer	Homooligomer	Protein 60	SULFATE ION × 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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1x9p
Deposition date deposition_date	2004-08-24
Structure title title	The crystal structure of human adenovirus 2 penton base
Keywords keywords	jellyroll domain, anti-parallel beta sheet, insertion domain, Virus like Particle; VIRUS LIKE PARTICLE
Experimental Method method	X-RAY DIFFRACTION

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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.

1x9p__assembly_1__model_1

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

Download this curve (.dat)

1x9p__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1x9p__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	99.88 Å
Rg (electron density)	99.32 Å
Total Rg	99.40 Å
Atom count	220620
Residues	27600
Excluded volume	3912500 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1x9p__assembly_1__model_1`	complete icosahedral assembly （60）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1x9p__assembly_2__model_1`	monomeric （1）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
3	1	`1x9p__assembly_3__model_1`	pentameric （5）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
4	1	`1x9p__assembly_4__model_1`	hexameric （6）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
5	1	`1x9p__assembly_5__model_1`	monomeric （1）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
6	1	`1x9p__assembly_6__model_1`	60-meric （60）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.

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4. Crystallography and Experiment 4. Crystallography & Experiment

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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	3677

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 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	1

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

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	1x9pA01
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	1x9pA02
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

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Unit-cell length a length_a	435.984 Å
Unit-cell length b length_b	300.168 Å
Unit-cell length c length_c	420.621 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	104.36 °
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	3.300 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.3070
R_work r_work	0.3070
R_free r_free	0.3070

The crystal structure of human adenovirus 2 penton base

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

1x9p__assembly_1__model_1

1x9p__assembly_1__model_1 | I(q)

1x9p__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-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

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

1x9p__assembly_1__model_1

1x9p__assembly_1__model_1 | I(q)

1x9p__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)