SAXSdb — 3ikj

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

V-type ATP synthase alpha chain

Pyrococcus horikoshii

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	(4S)-2-METHYL-2,4-PENTANEDIOL × 3 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	VATA_PYRHO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–240； UniProt 1–240 Author chain A； PDBConstruct 241–588； UniProt 617–964

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	3ikj
Deposition date deposition_date	2009-08-06
Structure title title	Structural characterization for the nucleotide binding ability of subunit A mutant S238A of the A1AO ATP synthase
Keywords keywords	HYDROLASE, A-Type ATP synthase mutant; HYDROLASE
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.

3ikj__assembly_1__model_1

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

Download this curve (.dat)

3ikj__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3ikj__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	27.08 Å
Rg (electron density)	26.59 Å
Total Rg	27.35 Å
Atom count	4087
Residues	513
Excluded volume	73537 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3ikj__assembly_1__model_1`	monomeric （1）	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	V-type ATP synthase alpha chain
Molecular weight formula_weight	65759.8 kDa
EC 编号 ec_number	3.6.3.14
Mutation mutation	G79R, S238A
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	4353

MVAKGRIIRVTGPLVVADGMKGAKMYEVVRVGELGLIGEIIRLEGDKAVIQVYEETAGVRPGEPVVGTGASLSVELGPRLLTSIYDGIQRPLEVIREKTGDFIARGVTAPALPRDKKWHFIPKAKVGDKVVGGDIIGEVPETSIIVHKIMVPPGIEGEIVEIAEEGDYTIEEVIAKVKTPSGEIKELKMYQRWPVRVKRPYKEKLPPEVPLITGQRVIDTFFPQAKGGTAAIPGPFGAGKTVTQHQLAKWSDAQVVIYIGCGERGNEMTDVLEEFPKLKDPKTGKPLMERTVLIANTSNMPVAAREASIYTGITIAEYFRDMGYDVALMADSTSRWAEALREISGRLEEMPGEEGYPAYLASKLAEFYERAGRVVTLGSDYRVGSVSVIGAVSPPGGDFSEPVVQNTLRVVKVFWALDADLARRRHFPAINWLTSYSLYVDAVKDWWHKNIDPEWKAMRDKAMALLQKESELQEIVRIVGPDALPERERAILLVARMLREDYLQQDAFDEVDTYCPPEKQVTMMRVLLNFYDKTMEAINRGVPLEEIAKLPVREEIGRMKFERDVSKIRSLIDKTNEQFEELFKKYGA

Source Source

Source organism organism	Pyrococcus horikoshii
NCBI taxonomy ID ncbi_taxonomy_id	70601
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	(4S)-2-METHYL-2,4-PENTANEDIOL
Molecular weight formula_weight	118.2 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 3 Entity 3 non-polymer

Description description	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Molecular weight formula_weight	122.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	266

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d3ikja1
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.37.1.11 — RecA protein-like (ATPase-domain)

Domain ID domain_id	d3ikja2
Class class	b — All beta proteins
Fold Fold fold	b.84 — Barrel-sandwich hybrid
Superfamily Superfamily superfamily	b.84.5 — V1 ATP synthase A subunit, bulge domain-like
Family Family family	b.84.5.1 — V1 ATP synthase A subunit, bulge domain-like

Domain ID domain_id	d3ikja3
Class class	a — All alpha proteins
Fold Fold fold	a.69 — Left-handed superhelix
Superfamily Superfamily superfamily	a.69.1 — C-terminal domain of alpha and beta (or A/B) subunits of rotary ATPases
Family Family family	a.69.1.2 — C-terminal domain of A and B subunits of V1 ATP synthase and A1 ATP sythase

CATH v4.4 (3 domains)

Domain ID domain_id	3ikjA01
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	3ikjA02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	100 — RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain

Domain ID domain_id	3ikjA03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1140 — Bovine Mitochondrial F1-ATPase, ATP Synthase Beta Chain; Chain D, domain3
Homologous superfamily homologous superfamily	10 — Bovine Mitochondrial F1-atpase; Atp Synthase Beta Chain; Chain D, domain 3

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Unit-cell length a length_a	128.214 Å
Unit-cell length b length_b	128.214 Å
Unit-cell length c length_c	105.825 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	29.840 Å
R factor r_factor	0.2427
R_work r_work	0.2394
R_free r_free	0.3036

Structural characterization for the nucleotide binding ability of subunit A mutant S238A of the A1AO ATP synthase

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

V-type ATP synthase alpha chain

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

3ikj__assembly_1__model_1

3ikj__assembly_1__model_1 | I(q)

3ikj__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) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

7. Citations (2)

Structural characterization for the nucleotide binding ability of subunit A mutant S238A of the A1AO ATP synthase

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

V-type ATP synthase alpha chain

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

3ikj__assembly_1__model_1

3ikj__assembly_1__model_1 | I(q)

3ikj__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) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

7. Citations (2)