SAXSdb — 2gb5

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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 water × 2	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 Author chain B； 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	2gb5
Deposition date deposition_date	2006-03-09
Structure title title	Crystal structure of NADH pyrophosphatase (EC 3.6.1.22) (1790429) from Escherichia coli K12 at 2.30 A resolution
Keywords keywords	;1790429, NADH pyrophosphatase (EC 3.6.1.22), Structural Genomics, PSI, Protein Structure Initiative, Joint Center for Structural Genomics, JCSG, 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.

2gb5__assembly_1__model_1

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

Download this curve (.dat)

2gb5__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2gb5__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	25.58 Å
Rg (electron density)	24.41 Å
Total Rg	25.12 Å
Atom count	4173
Residues	510
Excluded volume	73982 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2gb5__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 (3)

Entity 1 Entity 1 polymer

Description description	NADH pyrophosphatase
Molecular weight formula_weight	31608.6 kDa
EC 编号 ec_number	3.6.1.22
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	4458

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	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	240

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d2gb5a1
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	d2gb5a2
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	d2gb5a3
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	d2gb5a4
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

Domain ID domain_id	d2gb5b1
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	d2gb5b2
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	d2gb5b3
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	d2gb5b4
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 (4 domains)

Domain ID domain_id	2gb5A01
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	2gb5A02
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

Domain ID domain_id	2gb5B01
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	2gb5B02
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	99.287 Å
Unit-cell length b length_b	103.553 Å
Unit-cell length c length_c	57.270 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 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	49.610 Å
R factor r_factor	—
R_work r_work	0.1980
R_free r_free	0.2520

Crystal structure of NADH pyrophosphatase (EC 3.6.1.22) (1790429) from Escherichia coli K12 at 2.30 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

2gb5__assembly_1__model_1

2gb5__assembly_1__model_1 | I(q)

2gb5__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (8 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of NADH pyrophosphatase (EC 3.6.1.22) (1790429) from Escherichia coli K12 at 2.30 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

2gb5__assembly_1__model_1

2gb5__assembly_1__model_1 | I(q)

2gb5__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (8 domains)

CATH v4.4 (4 domains)

7. Citations (1)