6ehj

Human N-myristoyltransferase (NMT1) with Myristoyl-CoA and peptide bound

Method: X-RAY DIFFRACTION

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

Glycylpeptide N-tetradecanoyltransferase 1

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	GLYCEROL × 2 TETRADECANOYL-COA × 1 GLYCINE × 1 SERINE × 2 ASPARAGINE × 1 LYSINE × 3 PROLINE × 1 MYRISTIC ACID × 1 COENZYME A × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	GLYCEROL × 2 GLYCINE × 1 SERINE × 2 ASPARAGINE × 1 LYSINE × 3 PROLINE × 1 MYRISTIC ACID × 1 COENZYME A × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NMT1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–391； UniProt 109–496 Author chain B； PDBConstruct 4–391； UniProt 109–496

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	6ehj
Deposition date deposition_date	2017-09-13
Structure title title	Human N-myristoyltransferase (NMT1) with Myristoyl-CoA and peptide bound
Keywords keywords	Myristoylation, complex, substrate peptide, 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.

6ehj__assembly_1__model_1

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

Download this curve (.dat)

6ehj__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6ehj__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	22.18 Å
Rg (electron density)	20.83 Å
Total Rg	21.90 Å
Atom count	3113
Residues	371
Excluded volume	56067 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6ehj__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`6ehj__assembly_2__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 (11)

Entity 1 Entity 1 polymer

Description description	Glycylpeptide N-tetradecanoyltransferase 1
Molecular weight formula_weight	45453.3 kDa
EC 编号 ec_number	2.3.1.97
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	6609

GPHMEEASKRSYQFWDTQPVPKLGEVVNTHGPVEPDKDNIRQEPYTLPQGFTWDALDLGDRGVLKELYTLLNENYVEDDDNMFRFDYSPEFLLWALRPPGWLPQWHCGVRVVSSRKLVGFISAIPANIHIYDTEKKMVEINFLCVHKKLRSKRVAPVLIREITRRVHLEGIFQAVYTAGVVLPKPVGTCRYWHRSLNPRKLIEVKFSHLSRNMTMQRTMKLYRLPETPKTAGLRPMETKDIPVVHQLLTRYLKQFHLTPVMSQEEVEHWFYPQENIIDTFVVENANGEVTDFLSFYTLPSTIMNHPTHKSLKAAYSFYNVHTQTPLLDLMSDALVLAKMKGFDVFNALDLMENKTFLEKLKFGIGDGNLQYYLYNWKCPSMGAEKVGLVLQ

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

Entity 2 Entity 2 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	TETRADECANOYL-COA
Molecular weight formula_weight	977.9 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	GLYCINE
Molecular weight formula_weight	75.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	SERINE
Molecular weight formula_weight	105.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 6 Entity 6 non-polymer

Description description	ASPARAGINE
Molecular weight formula_weight	132.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 7 Entity 7 non-polymer

Description description	LYSINE
Molecular weight formula_weight	147.2 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 8 Entity 8 non-polymer

Description description	PROLINE
Molecular weight formula_weight	115.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 9 Entity 9 non-polymer

Description description	MYRISTIC ACID
Molecular weight formula_weight	228.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 10 Entity 10 non-polymer

Description description	COENZYME A
Molecular weight formula_weight	767.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 11 Entity 11 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	237

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d6ehja1
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	d6ehja2
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	d6ehjb1
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	d6ehjb2
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 (2 domains)

Domain ID domain_id	6ehjA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	630 — Aminopeptidase
Homologous superfamily homologous superfamily	170 —

Domain ID domain_id	6ehjB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	630 — Aminopeptidase
Homologous superfamily homologous superfamily	170 —

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Unit-cell length a length_a	80.250 Å
Unit-cell length b length_b	177.540 Å
Unit-cell length c length_c	58.140 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 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	47.080 Å
R factor r_factor	0.1870
R_work r_work	0.1843
R_free r_free	0.2386

Human N-myristoyltransferase (NMT1) with Myristoyl-CoA and peptide bound

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

Glycylpeptide N-tetradecanoyltransferase 1

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

6ehj__assembly_1__model_1

6ehj__assembly_1__model_1 | I(q)

6ehj__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 (11)

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 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 non-polymer

Entity 10 Entity 10 non-polymer

Entity 11 Entity 11 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Human N-myristoyltransferase (NMT1) with Myristoyl-CoA and peptide bound

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

Glycylpeptide N-tetradecanoyltransferase 1

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

6ehj__assembly_1__model_1

6ehj__assembly_1__model_1 | I(q)

6ehj__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 (11)

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 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 non-polymer

Entity 10 Entity 10 non-polymer

Entity 11 Entity 11 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

CATH v4.4 (2 domains)

7. Citations (1)