4b12

Plasmodium vivax N-myristoyltransferase with a bound benzofuran inhibitor (compound 23)

Method: X-RAY DIFFRACTION

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

GLYCYLPEPTIDE N-TETRADECANOYLTRANSFERASE

PLASMODIUM VIVAX

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	1-[3-methyl-4-(piperidin-4-yloxy)-1-benzofuran-2-yl]-3-phenylpropan-1-one × 1 2-oxopentadecyl-CoA × 1 DIMETHYL SULFOXIDE × 3 CHLORIDE ION × 1 MAGNESIUM ION × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	1-[3-methyl-4-(piperidin-4-yloxy)-1-benzofuran-2-yl]-3-phenylpropan-1-one × 1 2-oxopentadecyl-CoA × 1 DIMETHYL SULFOXIDE × 3 CHLORIDE ION × 1 MAGNESIUM ION × 1 SULFATE ION × 1 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	1-[3-methyl-4-(piperidin-4-yloxy)-1-benzofuran-2-yl]-3-phenylpropan-1-one × 1 2-oxopentadecyl-CoA × 1 DIMETHYL SULFOXIDE × 2 CHLORIDE ION × 1 MAGNESIUM ION × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A5K1A2_PLAVS
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–385； UniProt 27–410 Author chain B； PDBConstruct 2–385； UniProt 27–410 Author chain C； PDBConstruct 2–385； UniProt 27–410

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	4b12
Deposition date deposition_date	2012-07-06
Structure title title	Plasmodium vivax N-myristoyltransferase with a bound benzofuran inhibitor (compound 23)
Keywords keywords	TRANSFERASE, PLASMODIUM, MALARIA, DRUG DESIGN; 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.

4b12__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

4b12__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4b12__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	22.75 Å
Rg (electron density)	21.34 Å
Total Rg	22.44 Å
Atom count	3292
Residues	385
Excluded volume	59258 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4b12__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4b12__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`4b12__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 (8)

Entity 1 Entity 1 polymer

Description description	GLYCYLPEPTIDE N-TETRADECANOYLTRANSFERASE
Molecular weight formula_weight	45077.6 kDa
EC 编号 ec_number	2.3.1.97
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	11137

MDYKFWYTQPVPKINDEFNESVNEPFISDNKVEDVRKDEYKLPPGYSWYVCDVKDEKDRSEIYTLLTDNYVEDDDNIFRFNYSAEFLLWALTSPNYLKTWHIGVKYDASNKLIGFISAIPTDICIHKRTIKMAEVNFLCVHKTLRSKRLAPVLIKEITRRINLENIWQAIYTAGVYLPKPVSDARYYHRSINVKKLIEIGFSSLNSRLTMSRAIKLYRVEDTLNIKNMRLMKKKDVEGVHKLLGSYLEQFNLYAVFTKEEIAHWFLPIENVIYTYVNEENGKIKDMISFYSLPSQILGNDKYSTLNAAYSFYNVTTTATFKQLMQDAILLAKRNNFDVFNALEVMQNKSVFEDLKFGEGDGSLKYYLYNWKCASFAPAHVGIVLL

Source Source

Source organism organism	PLASMODIUM VIVAX
NCBI taxonomy ID ncbi_taxonomy_id	5855
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	1-[3-methyl-4-(piperidin-4-yloxy)-1-benzofuran-2-yl]-3-phenylpropan-1-one
Molecular weight formula_weight	363.4 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 3 Entity 3 non-polymer

Description description	2-oxopentadecyl-CoA
Molecular weight formula_weight	991.9 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 non-polymer

Description description	DIMETHYL SULFOXIDE
Molecular weight formula_weight	78.1 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 5 Entity 5 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 6 Entity 6 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 7 Entity 7 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1128

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6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id	4b12A00
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	4b12B00
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	4b12C00
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	57.470 Å
Unit-cell length b length_b	121.920 Å
Unit-cell length c length_c	178.250 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	1.790 Å
Low-resolution limit resolution_low	54.760 Å
R factor r_factor	0.1877
R_work r_work	0.1850
R_free r_free	0.2386

Plasmodium vivax N-myristoyltransferase with a bound benzofuran inhibitor (compound 23)

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

4b12__assembly_2__model_1

4b12__assembly_2__model_1 | I(q)

4b12__assembly_2__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 (8)

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 water

6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

7. Citations (1)

Plasmodium vivax N-myristoyltransferase with a bound benzofuran inhibitor (compound 23)

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

4b12__assembly_2__model_1

4b12__assembly_2__model_1 | I(q)

4b12__assembly_2__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 (8)

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 water

6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

7. Citations (1)