1suw

Crystal structure of a NAD kinase from Archaeoglobus fulgidus in complex with its substrate and product: Insights into the catalysis of NAD kinase

Method: X-RAY DIFFRACTION

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

Probable inorganic polyphosphate/ATP-NAD kinase

Archaeoglobus fulgidus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 4 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PPNK_ARCFU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–249； UniProt 1–249 Author chain B； PDBConstruct 1–249； UniProt 1–249 Author chain C； PDBConstruct 1–249； UniProt 1–249 Author chain D； PDBConstruct 1–249； UniProt 1–249

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	1suw
Deposition date deposition_date	2004-03-26
Structure title title	Crystal structure of a NAD kinase from Archaeoglobus fulgidus in complex with its substrate and product: Insights into the catalysis of NAD kinase
Keywords keywords	;ATP-NAD kinase, NADK, NAD, NADP, Structural Genomics, BSGC structure funded by NIH, Protein Structure Initiative, PSI, Berkeley Structural Genomics Center, 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.

1suw__assembly_1__model_1

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

Download this curve (.dat)

1suw__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1suw__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	32.05 Å
Rg (electron density)	31.29 Å
Total Rg	31.87 Å
Atom count	8048
Residues	996
Excluded volume	144540 Å³
Maximum q	0.500 Å⁻¹

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

Entity 1 Entity 1 polymer

Description description	Probable inorganic polyphosphate/ATP-NAD kinase
Molecular weight formula_weight	27905.4 kDa
EC 编号 ec_number	2.7.1.23
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	8351

MRAAVVYKTDGHVKRIEEALKRLEVEVELFNQPSEELENFDFIVSVGGDGTILRILQKLKRCPPIFGINTGRVGLLTHASPENFEVELKKAVEKFEVERFPRVSCSAMPDVLALNEIAVLSRKPAKMIDVALRVDGVEVDRIRCDGFIVATQIGSTGYAFSAGGPVVEPYLECFILIPIAPFRFGWKPYVVSMERKIEVIAEKAIVVADGQKSVDFDGEITIEKSEFPAVFFKNEKRFRNLFGKVRSIG

Source Source

Source organism organism	Archaeoglobus fulgidus
NCBI taxonomy ID ncbi_taxonomy_id	2234
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
Molecular weight formula_weight	743.4 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	303

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1suwa_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.52 — NAD kinase/diacylglycerol kinase-like
Superfamily Superfamily superfamily	e.52.1 — NAD kinase/diacylglycerol kinase-like
Family Family family	e.52.1.1 — NAD kinase-like

Domain ID domain_id	d1suwb_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.52 — NAD kinase/diacylglycerol kinase-like
Superfamily Superfamily superfamily	e.52.1 — NAD kinase/diacylglycerol kinase-like
Family Family family	e.52.1.1 — NAD kinase-like

Domain ID domain_id	d1suwc_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.52 — NAD kinase/diacylglycerol kinase-like
Superfamily Superfamily superfamily	e.52.1 — NAD kinase/diacylglycerol kinase-like
Family Family family	e.52.1.1 — NAD kinase-like

Domain ID domain_id	d1suwd_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.52 — NAD kinase/diacylglycerol kinase-like
Superfamily Superfamily superfamily	e.52.1 — NAD kinase/diacylglycerol kinase-like
Family Family family	e.52.1.1 — NAD kinase-like

CATH v4.4 (8 domains)

Domain ID domain_id	1suwA01
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	1suwA02
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

Domain ID domain_id	1suwB01
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	1suwB02
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

Domain ID domain_id	1suwC01
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	1suwC02
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

Domain ID domain_id	1suwD01
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	1suwD02
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	122.141 Å
Unit-cell length b length_b	122.141 Å
Unit-cell length c length_c	198.595 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	32

Space group space_group	P 41 21 2
Space-group number int_tables_number	92
Crystal system crystal_system	—

Resolution resolution	2.450 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2130
R_work r_work	0.2110
R_free r_free	0.2522

Crystal structure of a NAD kinase from Archaeoglobus fulgidus in complex with its substrate and product: Insights into the catalysis of NAD kinase

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

Probable inorganic polyphosphate/ATP-NAD kinase

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

1suw__assembly_1__model_1

1suw__assembly_1__model_1 | I(q)

1suw__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 (4 domains)

CATH v4.4 (8 domains)

7. Citations (1)

Crystal structure of a NAD kinase from Archaeoglobus fulgidus in complex with its substrate and product: Insights into the catalysis of NAD kinase

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

Probable inorganic polyphosphate/ATP-NAD kinase

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

1suw__assembly_1__model_1

1suw__assembly_1__model_1 | I(q)

1suw__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 (4 domains)

CATH v4.4 (8 domains)

7. Citations (1)