SAXSdb — 2h2a

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

Probable nicotinate-nucleotide adenylyltransferase

Staphylococcus aureus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	CALCIUM ION × 1 NICOTINIC ACID ADENINE DINUCLEOTIDE × 2 GLYCEROL × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NADD_STAAC
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–189； UniProt 1–189 Author chain B； PDBConstruct 1–189； UniProt 1–189

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	2h2a
Deposition date deposition_date	2006-05-18
Structure title title	Crystal structure of Nicotinic acid mononucleotide adenylyltransferase from Staphylococcus aureus: product bound form 2
Keywords keywords	NadD, NaMNAT, NMNAT, 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.

2h2a__assembly_1__model_1

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

Download this curve (.dat)

2h2a__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2h2a__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	24.00 Å
Rg (electron density)	23.28 Å
Total Rg	24.07 Å
Atom count	3211
Residues	376
Excluded volume	57137 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2h2a__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 (5)

Entity 1 Entity 1 polymer

Description description	Probable nicotinate-nucleotide adenylyltransferase
Molecular weight formula_weight	22171.3 kDa
EC 编号 ec_number	2.7.7.18
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	3381

MKKIVLYGGQFNPIHTAHMIVASEVFHELQPDEFYFLPSFMSPLKKHHDFIDVQHRLTMIQMIIDELGFGDICDDEIKRGGQSYTYDTIKAFKEQHKDSELYFVIGTDQYNQLEKWYQIEYLKEMVTFVVVNRDKNSQNVENAMIAIQIPRVDISSTMIRQRVSEGKSIQVLVPKSVENYIKGEGLYEH

Source Source

Source organism organism	Staphylococcus aureus
NCBI taxonomy ID ncbi_taxonomy_id	1280
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	NICOTINIC ACID ADENINE DINUCLEOTIDE
Molecular weight formula_weight	665.4 kDa
Source method src_method	syn
Copy count entity_count	2

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	170

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2h2aa_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.26 — Adenine nucleotide alpha hydrolase-like
Superfamily Superfamily superfamily	c.26.1 — Nucleotidylyl transferase
Family Family family	c.26.1.3 — Adenylyltransferase

Domain ID domain_id	d2h2ab_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.26 — Adenine nucleotide alpha hydrolase-like
Superfamily Superfamily superfamily	c.26.1 — Nucleotidylyl transferase
Family Family family	c.26.1.3 — Adenylyltransferase

CATH v4.4 (2 domains)

Domain ID domain_id	2h2aA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	620 — HUPs

Domain ID domain_id	2h2aB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	620 — HUPs

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Unit-cell length a length_a	62.303 Å
Unit-cell length b length_b	83.649 Å
Unit-cell length c length_c	99.113 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 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.2020
R_work r_work	0.2000
R_free r_free	0.2390

Crystal structure of Nicotinic acid mononucleotide adenylyltransferase from Staphylococcus aureus: product bound form 2

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

Probable nicotinate-nucleotide adenylyltransferase

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

2h2a__assembly_1__model_1

2h2a__assembly_1__model_1 | I(q)

2h2a__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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of Nicotinic acid mononucleotide adenylyltransferase from Staphylococcus aureus: product bound form 2

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

Probable nicotinate-nucleotide adenylyltransferase

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

2h2a__assembly_1__model_1

2h2a__assembly_1__model_1 | I(q)

2h2a__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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)