SAXSdb — 6hd3

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

Cell division control protein 48 homolog A

Arabidopsis thaliana

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 24	PHOSPHATE ION × 36 ADENOSINE-5'-DIPHOSPHATE × 24 water × 24	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CD48A_ARATH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–481； UniProt 1–481 Author chain C； PDBConstruct 1–481； UniProt 1–481

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	6hd3
Deposition date deposition_date	2018-08-17
Structure title title	Common mode of remodeling AAA ATPases p97/CDC48 by their disassembly cofactors ASPL/PUX1
Keywords keywords	ATPase, Arabidopsis thaliana, CDC48, hexamer, PLANT PROTEIN; PLANT PROTEIN
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.

6hd3__assembly_1__model_1

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

Download this curve (.dat)

6hd3__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6hd3__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	69.68 Å
Rg (electron density)	69.45 Å
Total Rg	69.53 Å
Atom count	83928
Residues	10620
Excluded volume	1490800 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6hd3__assembly_1__model_1`	24-meric （24）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Cell division control protein 48 homolog A
Molecular weight formula_weight	53671.2 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	7097

MSTPAESSDSKSKKDFSTAILERKKSPNRLVVDEAINDDNSVVSLHPATMEKLQLFRGDTILIKGKKRKDTVCIALADETCEEPKIRMNKVVRSNLRVRLGDVISVHQCPDVKYGKRVHILPVDDTVEGVTGNLFDAYLKPYFLEAYRPVRKGDLFLVRGGMRSVEFKVIETDPAEYCVVAPDTEIFCEGEPVKREDEERLDDVGYDDVGGVRKQMAQIRELVELPLRHPQLFKSIGVKPPKGILLYGPPGSGKTLIARAVANETGAFFFCINGPEIMSKLAGESESNLRKAFEEAEKNAPSIIFIDEIDSIAPKREKTNGEVERRIVSQLLTLMDGLKSRAHVIVMGATNRPNSIDPALRRFGRFDREIDIGVPDEIGRLEVLRIHTKNMKLAEDVDLERISKDTHGYVGADLAALCTEAALQCIREKMDVIDLEDDSIDAEILNSMAVTNEHFHTALGNSNPSALRETVVEVPNVSWND

Source Source

Source organism organism	Arabidopsis thaliana
Common name common_name	Mouse-ear cress
NCBI taxonomy ID ncbi_taxonomy_id	3702
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 3 Entity 3 non-polymer

Description description	ADENOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	427.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	96

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6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d6hd3c1
Class class	b — All beta proteins
Fold Fold fold	b.52 — Double psi beta-barrel
Superfamily Superfamily superfamily	b.52.2 — ADC-like
Family Family family	b.52.2.0 — automated matches

Domain ID domain_id	d6hd3c2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.31 — Cdc48 domain 2-like
Superfamily Superfamily superfamily	d.31.1 — Cdc48 domain 2-like
Family Family family	d.31.1.0 — automated matches

Domain ID domain_id	d6hd3c3
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.20 — Extended AAA-ATPase domain

CATH v4.4 (7 domains)

Domain ID domain_id	6hd3A01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	40 — Barwin-like endoglucanases
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	6hd3A02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	6hd3A03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	60 —

Domain ID domain_id	6hd3C01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	40 — Barwin-like endoglucanases
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	6hd3C02
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	330 — Vcp-like ATPase; Chain A, domain 2
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	6hd3C03
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	6hd3C04
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	60 —

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Unit-cell length a length_a	146.266 Å
Unit-cell length b length_b	146.266 Å
Unit-cell length c length_c	173.133 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	24

Space group space_group	P 6 2 2
Space-group number int_tables_number	177
Crystal system crystal_system	—

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	47.880 Å
R factor r_factor	0.2210
R_work r_work	0.2190
R_free r_free	0.2620

Common mode of remodeling AAA ATPases p97/CDC48 by their disassembly cofactors ASPL/PUX1

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

Cell division control protein 48 homolog A

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

6hd3__assembly_1__model_1

6hd3__assembly_1__model_1 | I(q)

6hd3__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (3 domains)

CATH v4.4 (7 domains)

7. Citations (1)

Common mode of remodeling AAA ATPases p97/CDC48 by their disassembly cofactors ASPL/PUX1

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

Cell division control protein 48 homolog A

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

6hd3__assembly_1__model_1

6hd3__assembly_1__model_1 | I(q)

6hd3__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (3 domains)

CATH v4.4 (7 domains)

7. Citations (1)