SAXSdb — 3v7w

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

Probable inorganic polyphosphate/ATP-NAD kinase 1

Listeria monocytogenes

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	5'-azido-5'-deoxyadenosine × 8 CITRIC ACID × 4 GLYCEROL × 4 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PPNK1_LISMO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–264； UniProt 1–264

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	3v7w
Deposition date deposition_date	2011-12-22
Structure title title	Crystal structure of NAD kinase 1 from Listeria monocytogenes in complex with 5'-azido-5'-deoxyadenosine
Keywords keywords	ligand-screening by crystallography, Two-domain kinase, Inorganic polyphosphate/ATP-NAD kinase 1, TRANSFERASE; TRANSFERASE
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.

3v7w__assembly_1__model_1

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

Download this curve (.dat)

3v7w__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3v7w__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	31.63 Å
Rg (electron density)	30.98 Å
Total Rg	31.59 Å
Atom count	8416
Residues	1040
Excluded volume	148640 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3v7w__assembly_1__model_1`	tetrameric （4）	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 (5)

Entity 1 Entity 1 polymer

Description description	Probable inorganic polyphosphate/ATP-NAD kinase 1
Molecular weight formula_weight	31045.3 kDa
EC 编号 ec_number	2.7.1.23
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	2232

MKYMITSKGDEKSDLLRLNMIAGFGEYDMEYDDVEPEIVISIGGDGTFLSAFHQYEERLDEIAFIGIHTGHLGFYADWRPAEADKLVKLLAKGEYQKVSYPLLKTTVKYGIGKKEATYLALNESTVKSSGGPFVVDVVINDIHFERFRGDGLCMSTPSGTTAYNKSLGGALMHPSIEAMQLTEMASINNRVYRTIGSPLVFPKHHVVSLQPVNDKDFQISVDHLSILHRDVQEIRYEVSAKKIHFARFRSFPFWRRVHDSFIEDLEHHHHHH

Source Source

Source organism organism	Listeria monocytogenes
NCBI taxonomy ID ncbi_taxonomy_id	1639
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	5'-azido-5'-deoxyadenosine
Molecular weight formula_weight	292.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	CITRIC ACID
Molecular weight formula_weight	192.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

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

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	89

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	3v7wA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10330 — Probable inorganic polyphosphate/atp-NAD kinase; domain 1

Domain ID domain_id	3v7wA02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	200 — Tumour Suppressor Smad4
Homologous superfamily homologous superfamily	30 — Probable inorganic polyphosphate/atp-NAD kinase; domain 2

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Unit-cell length a length_a	62.912 Å
Unit-cell length b length_b	74.026 Å
Unit-cell length c length_c	118.419 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	I 2 2 2
Space-group number int_tables_number	23
Crystal system crystal_system	—

Resolution resolution	2.010 Å
Low-resolution limit resolution_low	37.258 Å
R factor r_factor	0.1870
R_work r_work	0.1865
R_free r_free	0.2039

Crystal structure of NAD kinase 1 from Listeria monocytogenes in complex with 5'-azido-5'-deoxyadenosine

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

Probable inorganic polyphosphate/ATP-NAD kinase 1

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

3v7w__assembly_1__model_1

3v7w__assembly_1__model_1 | I(q)

3v7w__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 (5)

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 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of NAD kinase 1 from Listeria monocytogenes in complex with 5'-azido-5'-deoxyadenosine

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

Probable inorganic polyphosphate/ATP-NAD kinase 1

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

3v7w__assembly_1__model_1

3v7w__assembly_1__model_1 | I(q)

3v7w__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 (5)

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 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)