2p6f

Crystal structures of Saccharomyces cerevisiae N-myristoyltransferase with bound myristoyl-CoA and inhibitors

Method: X-RAY DIFFRACTION

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

Glycylpeptide N-tetradecanoyltransferase

Saccharomyces cerevisiae

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	TETRADECANOYL-COA × 1 (Z)-3-BENZYL-5-(2-HYDROXY-3-NITROBENZYLIDENE)-2-THIOXOTHIAZOLIDIN-4-ONE × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	TETRADECANOYL-COA × 1 (Z)-3-BENZYL-5-(2-HYDROXY-3-NITROBENZYLIDENE)-2-THIOXOTHIAZOLIDIN-4-ONE × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	TETRADECANOYL-COA × 1 (Z)-3-BENZYL-5-(2-HYDROXY-3-NITROBENZYLIDENE)-2-THIOXOTHIAZOLIDIN-4-ONE × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	TETRADECANOYL-COA × 1 (Z)-3-BENZYL-5-(2-HYDROXY-3-NITROBENZYLIDENE)-2-THIOXOTHIAZOLIDIN-4-ONE × 1	Consistent with protein count
5	Protein monomer	Monomer	Protein 1	TETRADECANOYL-COA × 1 (Z)-3-BENZYL-5-(2-HYDROXY-3-NITROBENZYLIDENE)-2-THIOXOTHIAZOLIDIN-4-ONE × 1	Consistent with protein count
6	Protein monomer	Monomer	Protein 1	TETRADECANOYL-COA × 1 (Z)-3-BENZYL-5-(2-HYDROXY-3-NITROBENZYLIDENE)-2-THIOXOTHIAZOLIDIN-4-ONE × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NMT_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–455； UniProt 1–455 Author chain B； PDBConstruct 1–455； UniProt 1–455 Author chain C； PDBConstruct 1–455； UniProt 1–455 Author chain D； PDBConstruct 1–455； UniProt 1–455 Author chain E； PDBConstruct 1–455； UniProt 1–455 Author chain F； PDBConstruct 1–455； UniProt 1–455

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	2p6f
Deposition date deposition_date	2007-03-18
Structure title title	Crystal structures of Saccharomyces cerevisiae N-myristoyltransferase with bound myristoyl-CoA and inhibitors
Keywords keywords	antifungal drug, non-peptidic inhibitor, 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.

2p6f__assembly_3__model_1

Assembly 3 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2p6f__assembly_3__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2p6f__assembly_3__model_1 | P(r) · Pending

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

Rg（Guinier）	23.37 Å
Rg (electron density)	22.06 Å
Total Rg	23.20 Å
Atom count	3666
Residues	436
Excluded volume	65745 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2p6f__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2p6f__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2p6f__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`2p6f__assembly_4__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`2p6f__assembly_5__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`2p6f__assembly_6__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 (3)

Entity 1 Entity 1 polymer

Description description	Glycylpeptide N-tetradecanoyltransferase
Molecular weight formula_weight	52911.4 kDa
EC 编号 ec_number	2.3.1.97
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	21988

MSEEDKAKKLENLLKLLQLNNDDTSKFTQEQKKAMKDHKFWRTQPVKDFDEKVVEEGPIDKPKTPEDISDKPLPLLSSFEWCSIDVDNKKQLEDVFVLLNENYVEDRDAGFRFNYTKEFFNWALKSPGWKKDWHIGVRVKETQKLVAFISAIPVTLGVRGKQVPSVEINFLCVHKQLRSKRLTPVLIKEITRRVNKCDIWHALYTAGIVLPAPVSTCRYTHRPLNWKKLYEVDFTGLPDGHTEEDMIAENALPAKTKTAGLRKLKKEDIDQVFELFKRYQSRFELIQIFTKEEFEHNFIGEESLPLDKQVIFSYVVEQPDGKITDFFSFYSLPFTILNNTKYKDLGIGYLYYYATDADFQFKDRFDPKATKALKTRLCELIYDACILAKNANMDVFNALTSQDNTLFLDDLKFGPGDGFLNFYLFNYRAKPITGGLNPDNSNDIKRRSNVGVVML

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	TETRADECANOYL-COA
Molecular weight formula_weight	977.9 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 3 Entity 3 non-polymer

Description description	(Z)-3-BENZYL-5-(2-HYDROXY-3-NITROBENZYLIDENE)-2-THIOXOTHIAZOLIDIN-4-ONE
Molecular weight formula_weight	372.4 kDa
Source method src_method	syn
Copy count entity_count	6

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6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

Domain ID domain_id	2p6fA01
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	2p6fA02
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	2p6fB01
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	2p6fB02
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	2p6fC01
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	2p6fC02
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	2p6fD01
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	2p6fD02
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	2p6fE01
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	2p6fE02
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	2p6fF01
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	2p6fF02
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	188.760 Å
Unit-cell length b length_b	151.492 Å
Unit-cell length c length_c	133.939 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	107.46 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	24

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	3.100 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2730
R_work r_work	0.2700
R_free r_free	0.3320

Crystal structures of Saccharomyces cerevisiae N-myristoyltransferase with bound myristoyl-CoA and inhibitors

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

Glycylpeptide N-tetradecanoyltransferase

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

2p6f__assembly_3__model_1

2p6f__assembly_3__model_1 | I(q)

2p6f__assembly_3__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

7. Citations (1)

Crystal structures of Saccharomyces cerevisiae N-myristoyltransferase with bound myristoyl-CoA and inhibitors

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

Glycylpeptide N-tetradecanoyltransferase

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

2p6f__assembly_3__model_1

2p6f__assembly_3__model_1 | I(q)

2p6f__assembly_3__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

7. Citations (1)