SAXSdb — 6wfg

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

N-alpha-acetyltransferase 50

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	COENZYME A × 1 ;(2S)-N-[(2S)-3-[1-(3-tert-butyl-1-methyl-1H-pyrazole-5-carbonyl)piperidin-4-yl]-1-(methylamino)-1-oxopropan-2-yl]-6-oxopiperidine-2-carboxamide ; × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	COENZYME A × 1 ;(2S)-N-[(2S)-3-[1-(3-tert-butyl-1-methyl-1H-pyrazole-5-carbonyl)piperidin-4-yl]-1-(methylamino)-1-oxopropan-2-yl]-6-oxopiperidine-2-carboxamide ; × 1 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	COENZYME A × 1 ;(2S)-N-[(2S)-3-[1-(3-tert-butyl-1-methyl-1H-pyrazole-5-carbonyl)piperidin-4-yl]-1-(methylamino)-1-oxopropan-2-yl]-6-oxopiperidine-2-carboxamide ; × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NAA50_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–171； UniProt 1–169 Author chain C； PDBConstruct 3–171； UniProt 1–169 Author chain E； PDBConstruct 3–171； UniProt 1–169

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	6wfg
Deposition date deposition_date	2020-04-03
Structure title title	Crystal structure of human Naa50 in complex with an inhibitor (compound 3) identified using DNA encoded library technology
Keywords keywords	N-alpha-acetyltransferase 50, Inhibitor complex, DNA encoded library, CoA, TRANSFERASE, TRANSFERASE-INHIBITOR complex; TRANSFERASE/INHIBITOR
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.

6wfg__assembly_1__model_1

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

Download this curve (.dat)

6wfg__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6wfg__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	16.33 Å
Rg (electron density)	14.91 Å
Total Rg	16.01 Å
Atom count	1340
Residues	150
Excluded volume	23277 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6wfg__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`6wfg__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`6wfg__assembly_3__model_1`	monomeric （1）	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	N-alpha-acetyltransferase 50
Molecular weight formula_weight	19571.5 kDa
EC 编号 ec_number	2.3.1.258,2.3.1.-
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,E
Atom count atom_count	4178

GSMKGSRIELGDVTPHNIKQLKRLNQVIFPVSYNDKFYKDVLEVGELAKLAYFNDIAVGAVCCRVDHSQNQKRLYIMTLGCLAPYRRLGIGTKMLNHVLNICEKDGTFDNIYLHVQISNESAIDFYRKFGFEIIETKKNYYKRIEPADAHVLQKNLKVPSGQNADVQKTDN

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	COENZYME A
Molecular weight formula_weight	767.5 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 3 Entity 3 non-polymer

Description description	;(2S)-N-[(2S)-3-[1-(3-tert-butyl-1-methyl-1H-pyrazole-5-carbonyl)piperidin-4-yl]-1-(methylamino)-1-oxopropan-2-yl]-6-oxopiperidine-2-carboxamide ;
Molecular weight formula_weight	474.6 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	142

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d6wfga_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.108 — Acyl-CoA N-acyltransferases (Nat)
Superfamily Superfamily superfamily	d.108.1 — Acyl-CoA N-acyltransferases (Nat)
Family Family family	d.108.1.0 — automated matches

Domain ID domain_id	d6wfgc_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.108 — Acyl-CoA N-acyltransferases (Nat)
Superfamily Superfamily superfamily	d.108.1 — Acyl-CoA N-acyltransferases (Nat)
Family Family family	d.108.1.0 — automated matches

Domain ID domain_id	d6wfge_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.108 — Acyl-CoA N-acyltransferases (Nat)
Superfamily Superfamily superfamily	d.108.1 — Acyl-CoA N-acyltransferases (Nat)
Family Family family	d.108.1.0 — automated matches

CATH v4.4 (3 domains)

Domain ID domain_id	6wfgA00
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	6wfgC00
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	6wfgE00
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)

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Unit-cell length a length_a	47.830 Å
Unit-cell length b length_b	102.940 Å
Unit-cell length c length_c	67.640 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	106.71 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.160 Å
Low-resolution limit resolution_low	64.790 Å
R factor r_factor	0.2030
R_work r_work	0.2010
R_free r_free	0.2530

Crystal structure of human Naa50 in complex with an inhibitor (compound 3) identified using DNA encoded library technology

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

N-alpha-acetyltransferase 50

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

6wfg__assembly_1__model_1

6wfg__assembly_1__model_1 | I(q)

6wfg__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) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

7. Citations (1)

Crystal structure of human Naa50 in complex with an inhibitor (compound 3) identified using DNA encoded library technology

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

N-alpha-acetyltransferase 50

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

6wfg__assembly_1__model_1

6wfg__assembly_1__model_1 | I(q)

6wfg__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) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

7. Citations (1)