1iyl

Crystal Structure of Candida albicans N-myristoyltransferase with Non-peptidic Inhibitor

Method: X-RAY DIFFRACTION

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

Myristoyl-CoA:Protein N-Myristoyltransferase

Candida albicans

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	(1-METHYL-1H-IMIDAZOL-2-YL)-(3-METHYL-4-{3-[(PYRIDIN-3-YLMETHYL)-AMINO]-PROPOXY}-BENZOFURAN-2-YL)-METHANONE × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	(1-METHYL-1H-IMIDAZOL-2-YL)-(3-METHYL-4-{3-[(PYRIDIN-3-YLMETHYL)-AMINO]-PROPOXY}-BENZOFURAN-2-YL)-METHANONE × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	(1-METHYL-1H-IMIDAZOL-2-YL)-(3-METHYL-4-{3-[(PYRIDIN-3-YLMETHYL)-AMINO]-PROPOXY}-BENZOFURAN-2-YL)-METHANONE × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	No other associated polymer	Consistent with protein count
5	Protein homooligomer	Homooligomer	Protein 2	(1-METHYL-1H-IMIDAZOL-2-YL)-(3-METHYL-4-{3-[(PYRIDIN-3-YLMETHYL)-AMINO]-PROPOXY}-BENZOFURAN-2-YL)-METHANONE × 2	Consistent with protein count
6	Protein homooligomer	Homooligomer	Protein 2	(1-METHYL-1H-IMIDAZOL-2-YL)-(3-METHYL-4-{3-[(PYRIDIN-3-YLMETHYL)-AMINO]-PROPOXY}-BENZOFURAN-2-YL)-METHANONE × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NMT_CANAL
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–392； UniProt 60–451 Author chain B； PDBConstruct 1–392； UniProt 60–451 Author chain C； PDBConstruct 1–392； UniProt 60–451 Author chain D； PDBConstruct 1–392； UniProt 60–451

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	1iyl
Deposition date deposition_date	2002-08-29
Structure title title	Crystal Structure of Candida albicans N-myristoyltransferase with Non-peptidic Inhibitor
Keywords keywords	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.

1iyl__assembly_1__model_1

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

Download this curve (.dat)

1iyl__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1iyl__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	23.07 Å
Rg (electron density)	21.76 Å
Total Rg	22.90 Å
Atom count	3178
Residues	384
Excluded volume	56890 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1iyl__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1iyl__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`1iyl__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`1iyl__assembly_4__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`1iyl__assembly_5__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`1iyl__assembly_6__model_1`	dimeric （2）	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 (2)

Entity 1 Entity 1 polymer

Description description	Myristoyl-CoA:Protein N-Myristoyltransferase
Molecular weight formula_weight	45421.6 kDa
EC 编号 ec_number	2.3.1.97
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	12597

EGPIDKLKTPEDVPNDPLPLISDFEWSTLDIDDNLQLDELYKLLYDNYVEDIDATFRFKYSHEFFQWALKPPGWRKDWHVGVRVKSTGKLVAFIAATPVTFKLNKSNKVIDSVEINFLCIHKKLRNKRLAPVLIKEITRRVNKQNIWQALYTGGSILPTPLTTCRYQHRPINWSKLHDVGFSHLPPNQTKSSMVASYTLPNNPKLKGLRPMTGKDVSTVLSLLYKYQERFDIVQLFTEEEFKHWMLGHDENSDSNVVKSYVVEDENGIITDYFSYYLLPFTVLDNAQHDELGIAYLFYYASDSFEKPNYKKRLNELITDALITSKKFGVDVFNCLTCQDNTYFLKDCKFGSGDGFLNYYLFNYRTFPMDGGIDKKTKEVVEDQTSGIGVVLL

Source Source

Source organism organism	Candida albicans
NCBI taxonomy ID ncbi_taxonomy_id	5476
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	(1-METHYL-1H-IMIDAZOL-2-YL)-(3-METHYL-4-{3-[(PYRIDIN-3-YLMETHYL)-AMINO]-PROPOXY}-BENZOFURAN-2-YL)-METHANONE
Molecular weight formula_weight	404.5 kDa
Source method src_method	syn
Copy count entity_count	3

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6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d1iyla1
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.108.1.2 — N-myristoyl transferase, NMT

Domain ID domain_id	d1iyla2
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.108.1.2 — N-myristoyl transferase, NMT

Domain ID domain_id	d1iylb1
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.108.1.2 — N-myristoyl transferase, NMT

Domain ID domain_id	d1iylb2
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.108.1.2 — N-myristoyl transferase, NMT

Domain ID domain_id	d1iylc1
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.108.1.2 — N-myristoyl transferase, NMT

Domain ID domain_id	d1iylc2
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.108.1.2 — N-myristoyl transferase, NMT

Domain ID domain_id	d1iyld1
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.108.1.2 — N-myristoyl transferase, NMT

Domain ID domain_id	d1iyld2
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.108.1.2 — N-myristoyl transferase, NMT

CATH v4.4 (8 domains)

Domain ID domain_id	1iylA01
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	1iylA02
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	1iylB01
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	1iylB02
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	1iylC01
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	1iylC02
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	1iylD01
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	1iylD02
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	93.277 Å
Unit-cell length b length_b	96.885 Å
Unit-cell length c length_c	269.277 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	16

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

Resolution resolution	3.200 Å
Low-resolution limit resolution_low	40.000 Å
R factor r_factor	0.2880
R_work r_work	0.2840
R_free r_free	0.3660

Crystal Structure of Candida albicans N-myristoyltransferase with Non-peptidic Inhibitor

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

Myristoyl-CoA:Protein N-Myristoyltransferase

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

1iyl__assembly_1__model_1

1iyl__assembly_1__model_1 | I(q)

1iyl__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (1)

Crystal Structure of Candida albicans N-myristoyltransferase with Non-peptidic Inhibitor

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

Myristoyl-CoA:Protein N-Myristoyltransferase

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

1iyl__assembly_1__model_1

1iyl__assembly_1__model_1 | I(q)

1iyl__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (1)