SAXSdb — 1vk6

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

NADH pyrophosphatase

Escherichia coli

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	ZINC ION × 2 (4S)-2-METHYL-2,4-PENTANEDIOL × 6 water × 2	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	ZINC ION × 1 (4S)-2-METHYL-2,4-PENTANEDIOL × 3 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NUDC_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 13–269； UniProt 1–257

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	1vk6
Deposition date deposition_date	2004-04-30
Structure title title	Crystal structure of NADH pyrophosphatase (1790429) from Escherichia coli k12 at 2.20 A resolution
Keywords keywords	;1790429, NADH PYROPHOSPHATASE, STRUCTURAL GENOMICS, JCSG, PSI, Protein Structure Initiative, Joint Center for Structural Genomics, 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.

1vk6__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

1vk6__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1vk6__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	22.61 Å
Rg (electron density)	21.45 Å
Total Rg	22.35 Å
Atom count	2078
Residues	249
Excluded volume	37071 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1vk6__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1vk6__assembly_2__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	NADH pyrophosphatase
Molecular weight formula_weight	31561.7 kDa
EC 编号 ec_number	3.6.1.-
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	2193

MGSDKIHHHHHHMDRIIEKLDHGWWVVSHEQKLWLPKGELPYGEAANFDLVGQRALQIGEWQGEPVWLVQQQRRHDMGSVRQVIDLDVGLFQLAGRGVQLAEFYRSHKYCGYCGHEMYPSKTEWAMLCSHCRERYYPQIAPCIIVAIRRDDSILLAQHTRHRNGVHTVLAGFVEVGETLEQAVAREVMEESGIKVKNLRYVTSQPWPFPQSLMTAFMAEYDSGDIVIDPKELLEANWYRYDDLPLLPPPGTVARRLIEDTVAMCRAEYE

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	83333
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 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 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) 6 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1vk6a2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.113 — Nudix
Superfamily Superfamily superfamily	d.113.1 — Nudix
Family Family family	d.113.1.4 — NADH pyrophosphatase

Domain ID domain_id	d1vk6a3
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.113 — Nudix
Superfamily Superfamily superfamily	d.113.1 — Nudix
Family Family family	d.113.1.4 — NADH pyrophosphatase

Domain ID domain_id	d1vk6a4
Class class	g — Small proteins
Fold Fold fold	g.41 — Rubredoxin-like
Superfamily Superfamily superfamily	g.41.14 — NADH pyrophosphatase intervening domain
Family Family family	g.41.14.1 — NADH pyrophosphatase intervening domain

Domain ID domain_id	d1vk6a5
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (2 domains)

Domain ID domain_id	1vk6A01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	79 — Nucleoside Triphosphate Pyrophosphohydrolase
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	1vk6A02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	79 — Nucleoside Triphosphate Pyrophosphohydrolase
Homologous superfamily homologous superfamily	10 — Nucleoside Triphosphate Pyrophosphohydrolase

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Unit-cell length a length_a	127.319 Å
Unit-cell length b length_b	127.319 Å
Unit-cell length c length_c	108.405 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	12

Space group space_group	P 65 2 2
Space-group number int_tables_number	179
Crystal system crystal_system	—

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	63.660 Å
R factor r_factor	0.1883
R_work r_work	0.1867
R_free r_free	0.2195

Crystal structure of NADH pyrophosphatase (1790429) from Escherichia coli k12 at 2.20 A resolution

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

NADH pyrophosphatase

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

1vk6__assembly_2__model_1

1vk6__assembly_2__model_1 | I(q)

1vk6__assembly_2__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 (4 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of NADH pyrophosphatase (1790429) from Escherichia coli k12 at 2.20 A resolution

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

NADH pyrophosphatase

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

1vk6__assembly_2__model_1

1vk6__assembly_2__model_1 | I(q)

1vk6__assembly_2__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 (4 domains)

CATH v4.4 (2 domains)

7. Citations (1)