SAXSdb — 4y49

▼

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

N-terminal acetyltransferase A complex subunit NAT1

Saccharomyces cerevisiae

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	N-terminal acetyltransferase A complex catalytic subunit ARD1 × 1 （P07347） N-terminal acetyltransferase A complex subunit NAT5 × 1 （Q08689） ALA-ALA-ALA-ALA-ALA-ALA × 1 GUANOSINE-5',3'-TETRAPHOSPHATE × 1 CARBOXYMETHYL COENZYME A × 1 ACETYL COENZYME A × 1	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	N-terminal acetyltransferase A complex catalytic subunit ARD1 × 1 （P07347） N-terminal acetyltransferase A complex subunit NAT5 × 1 （Q08689） ALA-ALA-ALA-ALA-ALA-ALA × 1 GUANOSINE-5',3'-TETRAPHOSPHATE × 1 CARBOXYMETHYL COENZYME A × 1 ACETYL COENZYME A × 1	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 4	N-terminal acetyltransferase A complex catalytic subunit ARD1 × 1 （P07347） N-terminal acetyltransferase A complex subunit NAT5 × 1 （Q08689） ALA-ALA-ALA-ALA-ALA-ALA × 1 GUANOSINE-5',3'-TETRAPHOSPHATE × 1 CARBOXYMETHYL COENZYME A × 1 ACETYL COENZYME A × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NAT1_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–854； UniProt 1–854 Author chain G； PDBConstruct 1–854； UniProt 1–854 Author chain M； PDBConstruct 1–854； UniProt 1–854

N-terminal acetyltransferase A complex catalytic subunit ARD1

Saccharomyces cerevisiae

UniProt P07347

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	N-terminal acetyltransferase A complex subunit NAT1 × 1 （P12945） N-terminal acetyltransferase A complex subunit NAT5 × 1 （Q08689） ALA-ALA-ALA-ALA-ALA-ALA × 1 GUANOSINE-5',3'-TETRAPHOSPHATE × 1 CARBOXYMETHYL COENZYME A × 1 ACETYL COENZYME A × 1	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	N-terminal acetyltransferase A complex subunit NAT1 × 1 （P12945） N-terminal acetyltransferase A complex subunit NAT5 × 1 （Q08689） ALA-ALA-ALA-ALA-ALA-ALA × 1 GUANOSINE-5',3'-TETRAPHOSPHATE × 1 CARBOXYMETHYL COENZYME A × 1 ACETYL COENZYME A × 1	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 4	N-terminal acetyltransferase A complex subunit NAT1 × 1 （P12945） N-terminal acetyltransferase A complex subunit NAT5 × 1 （Q08689） ALA-ALA-ALA-ALA-ALA-ALA × 1 GUANOSINE-5',3'-TETRAPHOSPHATE × 1 CARBOXYMETHYL COENZYME A × 1 ACETYL COENZYME A × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ARD1_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–238； UniProt 1–238 Author chain H； PDBConstruct 1–238； UniProt 1–238 Author chain N； PDBConstruct 1–238； UniProt 1–238

N-terminal acetyltransferase A complex subunit NAT5

Saccharomyces cerevisiae

UniProt Q08689

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	N-terminal acetyltransferase A complex subunit NAT1 × 1 （P12945） N-terminal acetyltransferase A complex catalytic subunit ARD1 × 1 （P07347） ALA-ALA-ALA-ALA-ALA-ALA × 1 GUANOSINE-5',3'-TETRAPHOSPHATE × 1 CARBOXYMETHYL COENZYME A × 1 ACETYL COENZYME A × 1	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	N-terminal acetyltransferase A complex subunit NAT1 × 1 （P12945） N-terminal acetyltransferase A complex catalytic subunit ARD1 × 1 （P07347） ALA-ALA-ALA-ALA-ALA-ALA × 1 GUANOSINE-5',3'-TETRAPHOSPHATE × 1 CARBOXYMETHYL COENZYME A × 1 ACETYL COENZYME A × 1	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 4	N-terminal acetyltransferase A complex subunit NAT1 × 1 （P12945） N-terminal acetyltransferase A complex catalytic subunit ARD1 × 1 （P07347） ALA-ALA-ALA-ALA-ALA-ALA × 1 GUANOSINE-5',3'-TETRAPHOSPHATE × 1 CARBOXYMETHYL COENZYME A × 1 ACETYL COENZYME A × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NAT5_YEAST
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–176； UniProt 1–176 Author chain I； PDBConstruct 1–176； UniProt 1–176 Author chain O； PDBConstruct 1–176； UniProt 1–176

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	4y49
Deposition date deposition_date	2015-02-10
Structure title title	Crystal structure of yeast N-terminal acetyltransferase (ppGpp) NatE in complex with a bisubstrate
Keywords keywords	N-terminal acetyltransferase, NatE, ppGpp, bisubstrate, TRANSFERASE; TRANSFERASE
Experimental Method method	X-RAY DIFFRACTION

▼

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.

4y49__assembly_1__model_1

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

Download this curve (.dat)

4y49__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4y49__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	34.37 Å
Rg (electron density)	33.79 Å
Total Rg	34.21 Å
Atom count	6716
Residues	1095
Excluded volume	112690 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4y49__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4y49__assembly_2__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`4y49__assembly_3__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Description description	N-terminal acetyltransferase A complex subunit NAT1
Molecular weight formula_weight	99084.2 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,G,M
Atom count atom_count	20122

MSRKRSTKPKPAAKIALKKYNDQFLEALKLYEGKQYKKSLKLLDAILKKDGSHVDSLALKGLDLYSVGEKDDAASYVANAIRKIEGASASPICCHVLGIYMRNTKEYKESIKWFTAALNNGSTNKQIYRDLATLQSQIGDFKNALVSRKKYWEAFLGYRANWTSLAVAQDVNGERQQAINTLSQFEKLAEGKISDSEKYEHSECLMYKNDIMYKAASDNQDKLQNVLKHLNDIEPCVFDKFGLLERKATIYMKLGQLKDASIVYRTLIKRNPDNFKYYKLLEVSLGIQGDNKLKKALYGKLEQFYPRCEPPKFIPLTFLQDKEELSKKLREYVLPQLERGVPATFSNVKPLYQRRKSKVSPLLEKIVLDYLSGLDPTQDPIPFIWTNYYLSQHFLFLKDFPKAQEYIDAALDHTPTLVEFYILKARILKHLGLMDTAAGILEEGRQLDLQDRFINCKTVKYFLRANNIDKAVEVASLFTKNDDSVNGIKDLHLVEASWFIVEQAEAYYRLYLDRKKKLDDLASLKKEVESDKSEQIANDIKENQWLVRKYKGLALKRFNAIPKFYKQFEDDQLDFHSYCMRKGTPRAYLEMLEWGKALYTKPMYVRAMKEASKLYFQMHDDRLKRKSDSLDENSDEIQNNGQNSSSQKKKAKKEAAAMNKRKETEAKSVAAYPSDQDNDVFGEKLIETSTPMEDFATEFYNNYSMQVREDERDYILDFEFNYRIGKLALCFASLNKFAKRFGTTSGLFGSMAIVLLHATRNDTPFDPILKKVVTKSLEKEYSENFPLNEISNNSFDWLNFYQEKFGKNDINGLLFLYRYRDDVPIGSSNLKEMIISSLSPLEPHSQNEILQYYL

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 polymer

Description description	N-terminal acetyltransferase A complex catalytic subunit ARD1
Molecular weight formula_weight	27635.2 kDa
EC 编号 ec_number	2.3.1.88
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,H,N

MPINIRRATINDIICMQNANLHNLPENYMMKYYMYHILSWPEASFVATTTTLDCEDSDEQDENDKLELTLDGTNDGRTIKLDPTYLAPGEKLVGYVLVKMNDDPDQQNEPPNGHITSLSVMRTYRRMGIAENLMRQALFALREVHQAEYVSLHVRQSNRAALHLYRDTLAFEVLSIEKSYYQDGEDAYAMKKVLKLEELQISNFTHRRLKENEEKLEDDLESDLLEDIIKQGVNDIIV

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 3 Entity 3 polymer

Description description	N-terminal acetyltransferase A complex subunit NAT5
Molecular weight formula_weight	19753.7 kDa
EC 编号 ec_number	2.3.1.-
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,I,O

MGRDICTLDNVYANNLGMLTKLAHVTVPNLYQDAFFSALFAEDSLVAKNKKPSSKKDVHFTQMAYYSEIPVGGLVAKLVPKKQNELSLKGIQIEFLGVLPNYRHKSIGSKLLKFAEDKCSECHQHNVFVYLPAVDDLTKQWFIAHGFEQVGETVNNFIKGVNGDEQDAILLKKHIS

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 4 Entity 4 polymer

Description description	ALA-ALA-ALA-ALA-ALA-ALA
Molecular weight formula_weight	1058.2 kDa
Source method src_method	syn
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,K,Q

SYSMEHFR

Entity 5 Entity 5 non-polymer

Description description	GUANOSINE-5',3'-TETRAPHOSPHATE
Molecular weight formula_weight	603.2 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 6 Entity 6 non-polymer

Description description	CARBOXYMETHYL COENZYME *A
Molecular weight formula_weight	825.6 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 7 Entity 7 non-polymer

Description description	ACETYL COENZYME *A
Molecular weight formula_weight	809.6 kDa
Source method src_method	syn
Copy count entity_count	3

▼

6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id	4y49B00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	630 — Aminopeptidase
Homologous superfamily homologous superfamily	30 — Gcn5-related N-acetyltransferase (GNAT)

Domain ID domain_id	4y49C00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	630 — Aminopeptidase
Homologous superfamily homologous superfamily	30 — Gcn5-related N-acetyltransferase (GNAT)

Domain ID domain_id	4y49H00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	630 — Aminopeptidase
Homologous superfamily homologous superfamily	30 — Gcn5-related N-acetyltransferase (GNAT)

Domain ID domain_id	4y49I00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	630 — Aminopeptidase
Homologous superfamily homologous superfamily	30 — Gcn5-related N-acetyltransferase (GNAT)

Domain ID domain_id	4y49N00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	630 — Aminopeptidase
Homologous superfamily homologous superfamily	30 — Gcn5-related N-acetyltransferase (GNAT)

Domain ID domain_id	4y49O00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	630 — Aminopeptidase
Homologous superfamily homologous superfamily	30 — Gcn5-related N-acetyltransferase (GNAT)

▶

Unit-cell length a length_a	111.723 Å
Unit-cell length b length_b	146.486 Å
Unit-cell length c length_c	254.107 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	12

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	3.950 Å
Low-resolution limit resolution_low	49.630 Å
R factor r_factor	0.3580
R_work r_work	0.3548
R_free r_free	0.4209

Crystal structure of yeast N-terminal acetyltransferase (ppGpp) NatE in complex with a bisubstrate

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

N-terminal acetyltransferase A complex subunit NAT1

State in the Current Structure

Other States of the Same Protein in the Database

N-terminal acetyltransferase A complex catalytic subunit ARD1

State in the Current Structure

Other States of the Same Protein in the Database

N-terminal acetyltransferase A complex subunit NAT5

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

4y49__assembly_1__model_1

4y49__assembly_1__model_1 | I(q)

4y49__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 (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)

Crystal structure of yeast N-terminal acetyltransferase (ppGpp) NatE in complex with a bisubstrate

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

N-terminal acetyltransferase A complex subunit NAT1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

N-terminal acetyltransferase A complex catalytic subunit ARD1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

N-terminal acetyltransferase A complex subunit NAT5

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

4y49__assembly_1__model_1

4y49__assembly_1__model_1 | I(q)

4y49__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 (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)