SAXSdb — 3aon

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

V-type sodium ATPase subunit G

Enterococcus hirae

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	V-type sodium ATPase subunit D × 1 NITRATE ION × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NTPG_ENTHR
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–103； UniProt 1–103

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	3aon
Deposition date deposition_date	2010-10-04
Structure title title	Crystal structure of the central axis (NtpD-NtpG) in the catalytic portion of Enterococcus hirae V-type sodium ATPase
Keywords keywords	V-ATPase, Enterococcus, Coiled-coil, Alpha/beta fold, Hydrolase, Na(+)-ATPase, NtpA3-NtpB3, NtpC, central axis; 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.

3aon__assembly_1__model_1

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

Download this curve (.dat)

3aon__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3aon__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	25.99 Å
Rg (electron density)	26.19 Å
Total Rg	26.58 Å
Atom count	2288
Residues	279
Excluded volume	41241 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3aon__assembly_1__model_1`	dimeric （2）	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 sodium ATPase subunit D
Molecular weight formula_weight	25588.0 kDa
EC 编号 ec_number	3.6.3.14
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	2454

GSSGSSGMRLNVNPTRMELTRLKKQLTTATRGHKLLKDKQDELMRQFILLIRKNNELRQAIEKETQTAMKDFVLAKSTVEEAFIDELLALPAENVSISVVEKNIMSVKVPLMNFQYDETLNETPLEYGYLHSNAELDRSIDGFTQLLPKLLKLAEVEKTCQLMAEEIEKTRRRVNALEYMTIPQLEETIYYIKMKLEENERAEVTRLIKVKNMGTEE

Source Source

Source organism organism	Enterococcus hirae
NCBI taxonomy ID ncbi_taxonomy_id	1354
Host organism host_organism	Cell free synthesis

Entity 2 Entity 2 polymer

Description description	V-type sodium ATPase subunit G
Molecular weight formula_weight	12783.1 kDa
EC 编号 ec_number	3.6.3.14
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MTYKIGVVGDKDSVSPFRLFGFDVQHGTTKTEIRKTIDEMAKNEYGVIYITEQCANLVPETIERYKGQLTPAIILIPSHQGTLGIGLEEIQNSVEKAVGQNILSGPSSGENLYFQ

Source Source

Source organism organism	Enterococcus hirae
NCBI taxonomy ID ncbi_taxonomy_id	1354
Host organism host_organism	Cell free synthesis

Entity 3 Entity 3 non-polymer

Description description	NITRATE ION
Molecular weight formula_weight	62.0 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	152

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6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d3aona_
Class class	h — Coiled coil proteins
Fold Fold fold	h.4 — Antiparallel coiled-coil
Superfamily Superfamily superfamily	h.4.20 — V-type ATPase central rotor subunit D
Family Family family	h.4.20.0 — automated matches

CATH v4.4 (2 domains)

Domain ID domain_id	3aonA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	3240 —

Domain ID domain_id	3aonB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10580 — ATPase, V1 complex, subunit F

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Unit-cell length a length_a	105.787 Å
Unit-cell length b length_b	68.433 Å
Unit-cell length c length_c	51.153 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	114.99 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	31.980 Å
R factor r_factor	0.1974
R_work r_work	0.1945
R_free r_free	0.2516

Crystal structure of the central axis (NtpD-NtpG) in the catalytic portion of Enterococcus hirae V-type sodium ATPase

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

V-type sodium ATPase subunit G

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

3aon__assembly_1__model_1

3aon__assembly_1__model_1 | I(q)

3aon__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 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of the central axis (NtpD-NtpG) in the catalytic portion of Enterococcus hirae V-type sodium ATPase

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

V-type sodium ATPase subunit G

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

3aon__assembly_1__model_1

3aon__assembly_1__model_1 | I(q)

3aon__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 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

CATH v4.4 (2 domains)

7. Citations (1)