SAXSdb — 3c2v

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

Nicotinate-nucleotide pyrophosphorylase

Saccharomyces cerevisiae

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 6	1-O-pyrophosphono-5-O-phosphono-alpha-D-ribofuranose × 6 PHTHALIC ACID × 6 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NADC_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–294； UniProt 2–295

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	3c2v
Deposition date deposition_date	2008-01-25
Structure title title	Crystal structure of the quinolinate phosphoribosyl transferase (BNA6) from Saccharomyces cerevisiae complexed with PRPP and the inhibitor phthalate
Keywords keywords	;QPRTase, PRTase, BNA6, quinolinate, phthalate, PRPP, Cytoplasm, Glycosyltransferase, Nucleus, Pyridine nucleotide biosynthesis, 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.

3c2v__assembly_1__model_1

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

Download this curve (.dat)

3c2v__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3c2v__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	34.30 Å
Rg (electron density)	33.43 Å
Total Rg	34.13 Å
Atom count	12606
Residues	1620
Excluded volume	223920 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3c2v__assembly_1__model_1`	hexameric （6）	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	Nicotinate-nucleotide pyrophosphorylase
Molecular weight formula_weight	32270.7 kDa
EC 编号 ec_number	2.4.2.19
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	2250

PVYEHLLPVNGAWRQDVTNWLSEDVPSFDFGGYVVGSDLKEANLYCKQDGMLCGVPFAQEVFNQCELQVEWLFKEGSFLEPSKNDSGKIVVAKITGPAKNILLAERTALNILSRSSGIATASHKIISLARSTGYKGTIAGTRKTTPGLRRLEKYSMLVGGCDTHRYDLSSMVMLKDNHIWATGSITNAVKNARAVCGFAVKIEVECLSEDEATEAIEAGADVIMLDNFKGDGLKMCAQSLKNKWNGKKHFLLECSGGLNLDNLEEYLCDDIDIYSTSSIHQGTPVIDFSLKLAH

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	1-O-pyrophosphono-5-O-phosphono-alpha-D-ribofuranose
Molecular weight formula_weight	390.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	PHTHALIC ACID
Molecular weight formula_weight	166.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	149

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	3c2vA01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1170 — Aldehyde Oxidoreductase; domain 3
Homologous superfamily homologous superfamily	20 — Quinolinate phosphoribosyl transferase, N-terminal domain

Domain ID domain_id	3c2vA02
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	70 — Aldolase class I

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Unit-cell length a length_a	154.668 Å
Unit-cell length b length_b	154.668 Å
Unit-cell length c length_c	69.346 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	18

Space group space_group	H 3 2
Space-group number int_tables_number	155
Crystal system crystal_system	—

Resolution resolution	2.290 Å
Low-resolution limit resolution_low	44.630 Å
R factor r_factor	0.2270
R_work r_work	0.2250
R_free r_free	0.2820

Crystal structure of the quinolinate phosphoribosyl transferase (BNA6) from Saccharomyces cerevisiae complexed with PRPP and the inhibitor phthalate

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

Nicotinate-nucleotide pyrophosphorylase

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

3c2v__assembly_1__model_1

3c2v__assembly_1__model_1 | I(q)

3c2v__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 (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) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of the quinolinate phosphoribosyl transferase (BNA6) from Saccharomyces cerevisiae complexed with PRPP and the inhibitor phthalate

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

Nicotinate-nucleotide pyrophosphorylase

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

3c2v__assembly_1__model_1

3c2v__assembly_1__model_1 | I(q)

3c2v__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 (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) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)