SAXSdb — 1ytk

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

nicotinate phosphoribosyltransferase from Thermoplasma acidophilum

Thermoplasma acidophilum

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 6	NICOTINATE MONONUCLEOTIDE × 6 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 6 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9HJ28_THEAC
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 7–398； UniProt 1–392

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	1ytk
Deposition date deposition_date	2005-02-10
Structure title title	Crystal structure of a nicotinate phosphoribosyltransferase from Thermoplasma acidophilum with nicotinate mononucleotide
Keywords keywords	;nicotinate phosphoribosyltransferase, type II phosphoribosyltransferase, zinc-knuckle motif, Structural Genomics, PSI, Protein Structure Initiative, Berkeley Structural Genomics Center, BSGC, 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.

1ytk__assembly_1__model_1

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

Download this curve (.dat)

1ytk__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1ytk__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	43.25 Å
Rg (electron density)	42.43 Å
Total Rg	42.90 Å
Atom count	18246
Residues	2334
Excluded volume	326090 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1ytk__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 phosphoribosyltransferase from Thermoplasma acidophilum
Molecular weight formula_weight	43695.1 kDa
EC 编号 ec_number	2.4.2.11
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	3105

GGGGGGMNVFNTASDEDIKKGLASDVYFERTISAIGDKCNDLRVAMEATVSGPLDTWINFTGLDEVLKLLEGLDVDLYAIPEGTILFPRDANGLPVPFIRVEGRYCDFGMYETAILGFICQASGISTKASKVRLAAGDSPFFSFGIRRMHPAISPMIDRSAYIGGADGVSGILGAKLIDQDPVGTMPHALSIMLGDEEAWKLTLENTKNGQKSVLLIDTYMDEKFAAIKIAEMFDKVDYIRLDTPSSRRGNFEALIREVRWELALRGRSDIKIMVSGGLDENTVKKLREAGAEAFGVGTSISSAKPFDFAMDIVEVNGKPETKRGKMSGRKNVLRCTSCHRIEVVPANVQEKTCICGGSMQNLLVKYLSHGKRTSEYPRPKEIRSRSMKELEYFKDIS

Source Source

Source organism organism	Thermoplasma acidophilum
NCBI taxonomy ID ncbi_taxonomy_id	273075
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	NICOTINATE MONONUCLEOTIDE
Molecular weight formula_weight	335.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Molecular weight formula_weight	122.1 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	64

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1ytka1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.41 — alpha/beta-Hammerhead
Superfamily Superfamily superfamily	d.41.2 — Nicotinate/Quinolinate PRTase N-terminal domain-like
Family Family family	d.41.2.1 — NadC N-terminal domain-like

Domain ID domain_id	d1ytka2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.17 — Nicotinate/Quinolinate PRTase C-terminal domain-like
Family Family family	c.1.17.1 — NadC C-terminal domain-like

CATH v4.4 (2 domains)

Domain ID domain_id	1ytkA01
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	1ytkA02
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	135.191 Å
Unit-cell length b length_b	135.191 Å
Unit-cell length c length_c	119.660 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	12

Space group space_group	P 63 2 2
Space-group number int_tables_number	182
Crystal system crystal_system	—

Resolution resolution	2.650 Å
Low-resolution limit resolution_low	19.990 Å
R factor r_factor	0.2010
R_work r_work	0.2010
R_free r_free	0.2530

Crystal structure of a nicotinate phosphoribosyltransferase from Thermoplasma acidophilum with nicotinate mononucleotide

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

nicotinate phosphoribosyltransferase from Thermoplasma acidophilum

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

1ytk__assembly_1__model_1

1ytk__assembly_1__model_1 | I(q)

1ytk__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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of a nicotinate phosphoribosyltransferase from Thermoplasma acidophilum with nicotinate mononucleotide

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

nicotinate phosphoribosyltransferase from Thermoplasma acidophilum

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

1ytk__assembly_1__model_1

1ytk__assembly_1__model_1 | I(q)

1ytk__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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)