8vka

Crystal structure of Plasmodium vivax glycylpeptide N-tetradecanoyltransferase (N-myristoyltransferase, NMT) bound to myristoyl-CoA and inhibitor 9c

Method: X-RAY DIFFRACTION

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

Glycylpeptide N-tetradecanoyltransferase

Plasmodium vivax Sal-1

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 N-[1,5-dimethyl-4-(2-{[(2M)-2'-(piperazin-1-yl)[2,4'-bipyridin]-3-yl]oxy}ethyl)-1H-pyrazole-3-carbonyl]glycine × 1 CHLORIDE ION × 13 GLYCEROL × 1 PENTAETHYLENE GLYCOL × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	TETRADECANOYL-COA × 1 N-[1,5-dimethyl-4-(2-{[(2M)-2'-(piperazin-1-yl)[2,4'-bipyridin]-3-yl]oxy}ethyl)-1H-pyrazole-3-carbonyl]glycine × 1 CHLORIDE ION × 4 GLYCEROL × 1 MAGNESIUM ION × 1 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	TETRADECANOYL-COA × 1 N-[1,5-dimethyl-4-(2-{[(2M)-2'-(piperazin-1-yl)[2,4'-bipyridin]-3-yl]oxy}ethyl)-1H-pyrazole-3-carbonyl]glycine × 1 CHLORIDE ION × 7 GLYCEROL × 1 PENTAETHYLENE GLYCOL × 1 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL × 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 3–386； UniProt 27–410 Author chain B； PDBConstruct 3–386； UniProt 27–410 Author chain C； PDBConstruct 3–386； 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	8vka
Deposition date deposition_date	2024-01-08
Last revision last_revision	2024-07-17
Structure title title	Crystal structure of Plasmodium vivax glycylpeptide N-tetradecanoyltransferase (N-myristoyltransferase, NMT) bound to myristoyl-CoA and inhibitor 9c
Keywords keywords	Enzyme, Inhibitor, Complex, Structural Genomics, Seattle Structural Genomics Center for Infectious Disease, SSGCID, 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.

8vka__assembly_1__model_1

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

Download this curve (.dat)

8vka__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8vka__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	23.00 Å
Rg (electron density)	21.59 Å
Total Rg	22.81 Å
Atom count	6543
Residues	384
Excluded volume	59201 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8vka__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`8vka__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`8vka__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 (9)

Entity 1 Entity 1 polymer

Description description	Glycylpeptide N-tetradecanoyltransferase
Molecular weight formula_weight	45100.6 kDa
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	22204

GPDYKFWYTQPVPKINDEFNESVNEPFISDNKVEDVRKDEYKLPPGYSWYVCDVKDEKDRSEIYTLLTDNYVEDDDNIFRFNYSAEFLLWALTSPNYLKTWHIGVKYDASNKLIGFISAIPTDICIHKRTIKMAEVNFLCVHKTLRSKRLAPVLIKEITRRINLENIWQAIYTAGVYLPKPVSDARYYHRSINVKKLIEIGFSSLNSRLTMSRAIKLYRVEDTLNIKNMRLMKKKDVEGVHKLLGSYLEQFNLYAVFTKEEIAHWFLPIENVIYTYVNEENGKIKDMISFYSLPSQILGNDKYSTLNAAYSFYNVTTTATFKQLMQDAILLAKRNNFDVFNALEVMQNKSVFEDLKFGEGDGSLKYYLYNWKCASFAPAHVGIVLL

Source Source

Source organism organism	Plasmodium vivax Sal-1
NCBI taxonomy ID ncbi_taxonomy_id	126793
Host organism host_organism	Escherichia coli BL21(DE3)

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	3

Entity 3 Entity 3 non-polymer

Description description	N-[1,5-dimethyl-4-(2-{[(2M)-2'-(piperazin-1-yl)[2,4'-bipyridin]-3-yl]oxy}ethyl)-1H-pyrazole-3-carbonyl]glycine
Molecular weight formula_weight	479.5 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	24

Entity 5 Entity 5 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 6 Entity 6 non-polymer

Description description	PENTAETHYLENE GLYCOL
Molecular weight formula_weight	238.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 7 Entity 7 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 8 Entity 8 non-polymer

Description description	3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL
Molecular weight formula_weight	326.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 9 Entity 9 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	951

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Unit-cell length a length_a	58.340 Å
Unit-cell length b length_b	119.279 Å
Unit-cell length c length_c	173.755 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	orthorhombic

Resolution resolution	1.970 Å
Low-resolution limit resolution_low	44.870 Å
R factor r_factor	0.1593
R_work r_work	0.1574
R_free r_free	0.1980

Crystal structure of Plasmodium vivax glycylpeptide N-tetradecanoyltransferase (N-myristoyltransferase, NMT) bound to myristoyl-CoA and inhibitor 9c

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

8vka__assembly_1__model_1

8vka__assembly_1__model_1 | I(q)

8vka__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 (9)

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 water

7. Citations (1)

Crystal structure of Plasmodium vivax glycylpeptide N-tetradecanoyltransferase (N-myristoyltransferase, NMT) bound to myristoyl-CoA and inhibitor 9c

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

8vka__assembly_1__model_1

8vka__assembly_1__model_1 | I(q)

8vka__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 (9)

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 water

7. Citations (1)