7dqd

Crystal structure of the AMP-PNP-bound mutant A(S23C)3B(N64C)3 complex from enterococcus hirae V-ATPase

Method: X-RAY DIFFRACTION

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

V-type sodium ATPase catalytic subunit A

Enterococcus hirae (strain ATCC 9790 / DSM 20160 / JCM 8729 / LMG 6399 / NBRC 3181 / NCIMB 6459 / NCDO 1258)

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	V-type sodium ATPase subunit B × 3 （Q08637） GLYCEROL × 1 PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 2 MAGNESIUM ION × 2 water × 4	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 6	V-type sodium ATPase subunit B × 3 （Q08637） PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 2 MAGNESIUM ION × 2 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NTPA_ENTHA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 8–600； UniProt 1–593 Author chain B； PDBConstruct 8–600； UniProt 1–593 Author chain C； PDBConstruct 8–600； UniProt 1–593 Author chain I； PDBConstruct 8–600； UniProt 1–593 Author chain J； PDBConstruct 8–600； UniProt 1–593 Author chain K； PDBConstruct 8–600； UniProt 1–593

V-type sodium ATPase subunit B

Enterococcus hirae (strain ATCC 9790 / DSM 20160 / JCM 8729 / LMG 6399 / NBRC 3181 / NCIMB 6459 / NCDO 1258)

UniProt Q08637

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	V-type sodium ATPase catalytic subunit A × 3 （Q08636） GLYCEROL × 1 PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 2 MAGNESIUM ION × 2 water × 4	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 6	V-type sodium ATPase catalytic subunit A × 3 （Q08636） PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 2 MAGNESIUM ION × 2 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NTPB_ENTHA
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain D； PDBConstruct 8–465； UniProt 1–458 Author chain E； PDBConstruct 8–465； UniProt 1–458 Author chain F； PDBConstruct 8–465； UniProt 1–458 Author chain L； PDBConstruct 8–465； UniProt 1–458 Author chain M； PDBConstruct 8–465； UniProt 1–458 Author chain N； PDBConstruct 8–465； UniProt 1–458

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	7dqd
Deposition date deposition_date	2020-12-23
Structure title title	Crystal structure of the AMP-PNP-bound mutant A(S23C)3B(N64C)3 complex from enterococcus hirae V-ATPase
Keywords keywords	V-ATPase, A3B3, asymmetric structure, HYDROLASE; 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.

7dqd__assembly_1__model_1

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

Download this curve (.dat)

7dqd__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7dqd__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	43.89 Å
Rg (electron density)	43.11 Å
Total Rg	43.50 Å
Atom count	23321
Residues	3097
Excluded volume	412420 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7dqd__assembly_1__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`7dqd__assembly_2__model_1`	hexameric （6）	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 (6)

Entity 1 Entity 1 polymer

Description description	V-type sodium ATPase catalytic subunit A
Molecular weight formula_weight	66363.9 kDa
EC 编号 ec_number	7.2.2.1
Mutation mutation	S23C
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,I,J,K
Atom count atom_count	46492

GSSGSSGMQIGKIIKVSGPLVMAENMSEACIQDMCLVGDLGVIGEIIEMRQDVASIQVYEETSGIGPGEPVRSTGEALSVELGPGIISQMFDGIQRPLDTFMEVTQSNFLGRGVQLPALDHEKQWWFEATIEEGTEVSAGDIIGYVDETKIIQHKIMVPNGIKGTVQKIESGSFTIDDPICVIETEQGLKELTMMQKWPVRRGRPIKQKLNPDVPMITGQRVIDTFFPVTKGGAAAVPGPFGAGKTVVQHQIAKWSDVDLVVYVGCGERGNEMTDVVNEFPELIDPNTGESLMERTVLIANTSNMPVAAREASIYTGITIAEYFRDMGYDVAIMADSTSRWAEALREMSGRLEEMPGDEGYPAYLGSRLAEYYERSGRVIALGSDQREGSITAISAVSPSGGDISEPVTQNTLRVVKVFWGLDSSLAQKRHFPSINWIQSYSLYSTEVGRYMDQILQQDWSDMVTEGMRILQEEEQLNEIVRLVGIDSLSDNDRLTLEVAKSIREDYLQQNAFDDVDTFTSREKQFNMLKVILTFGKEARKALSLGAYFNEIMEGTVAVRERISRSKYIPEEELAKISSINEEIKETIQLIVSEGGMTDD

Source Source

Source organism organism	Enterococcus hirae (strain ATCC 9790 / DSM 20160 / JCM 8729 / LMG 6399 / NBRC 3181 / NCIMB 6459 / NCDO 1258)
NCBI taxonomy ID ncbi_taxonomy_id	768486
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	V-type sodium ATPase subunit B
Molecular weight formula_weight	51709.9 kDa
Mutation mutation	N64C
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,E,F,L,M,N

GSSGSSGMIKEYRTIKEVVGPLMAVEKVSGVKYEELIEVRMQNGEIRRGQVLEVQEDKAMVQIFEGTSGICLKNSSVRFLGHPLQLGVSEDMIGRVFDGLGRPKDNGPEILPEKYLDINGEVINPIARDYPDEFIQTGISAIDHLNTLVRGQKLPVFSGSGLPHKELAAQIARQATVLDSSDDFAVVFAAIGITFEEAEFFMEDFRQTGAIDRSVMFMNLANDPAIERIATPRMALTAAEYLAYEKGMHVLVIMTDMTNYAEALREISAARREVPGRRGYPGYLYTNLATLFERAGRIRGLKGSVTQIPILTMPEDDKTHPIPDLTGYITEGQIILTRELYKSGIQPPIDVLPSLSRLKDKGTGAGKTREDHAATMNQLFAAYAQGKQAKELAVVLGESALSDIDKIYAKFAERFENEYVNQGFYTNRTITETLDLGWELLAMLPRTELKRIKDDLLDKYLPEGK

Source Source

Source organism organism	Enterococcus hirae (strain ATCC 9790 / DSM 20160 / JCM 8729 / LMG 6399 / NBRC 3181 / NCIMB 6459 / NCDO 1258)
NCBI taxonomy ID ncbi_taxonomy_id	768486
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
Molecular weight formula_weight	506.2 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	12

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6. Fold Classification (SCOP + CATH) 14 domains

CATH v4.4 (14 domains)

Domain ID domain_id	7dqdA01
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	7dqdA02
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

Domain ID domain_id	7dqdB01
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	7dqdB02
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

Domain ID domain_id	7dqdC01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	7dqdC02
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	7dqdC03
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

Domain ID domain_id	7dqdI01
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	7dqdI02
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

Domain ID domain_id	7dqdJ01
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	7dqdJ02
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

Domain ID domain_id	7dqdK01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	7dqdK02
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	7dqdK03
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	117.570 Å
Unit-cell length b length_b	123.380 Å
Unit-cell length c length_c	230.280 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.07 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	3.383 Å
Low-resolution limit resolution_low	49.365 Å
R factor r_factor	0.2622
R_work r_work	0.2609
R_free r_free	0.2856

Crystal structure of the AMP-PNP-bound mutant A(S23C)3B(N64C)3 complex from enterococcus hirae V-ATPase

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

V-type sodium ATPase catalytic subunit A

State in the Current Structure

Other States of the Same Protein in the Database

V-type sodium ATPase subunit B

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

7dqd__assembly_1__model_1

7dqd__assembly_1__model_1 | I(q)

7dqd__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 (6)

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 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 14 domains

CATH v4.4 (14 domains)

7. Citations (1)

Crystal structure of the AMP-PNP-bound mutant A(S23C)3B(N64C)3 complex from enterococcus hirae V-ATPase

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

V-type sodium ATPase catalytic subunit 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

V-type sodium ATPase subunit B

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

7dqd__assembly_1__model_1

7dqd__assembly_1__model_1 | I(q)

7dqd__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 (6)

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 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 14 domains

CATH v4.4 (14 domains)

7. Citations (1)