6nxg

Crystal structure of glycylpeptide N-tetradecanoyltransferase from Plasmodium vivax in complex with inhibitor 303a

Method: X-RAY DIFFRACTION

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

Glycylpeptide N-tetradecanoyltransferase

Plasmodium vivax (strain Salvador I)

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	MAGNESIUM ION × 1 CHLORIDE ION × 1 OXAMIC ACID × 1 5-(4-chlorophenyl)-3-({[3-(morpholine-4-carbonyl)phenyl]amino}methyl)pyridin-2(1H)-one × 1 TETRADECANOYL-COA × 1 BETA-MERCAPTOETHANOL × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	MAGNESIUM ION × 1 CHLORIDE ION × 1 5-(4-chlorophenyl)-3-({[3-(morpholine-4-carbonyl)phenyl]amino}methyl)pyridin-2(1H)-one × 1 TETRADECANOYL-COA × 1 BETA-MERCAPTOETHANOL × 1 1,2-ETHANEDIOL × 1 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	MAGNESIUM ION × 1 CHLORIDE ION × 1 TETRADECANOYL-COA × 1 BETA-MERCAPTOETHANOL × 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 22–405； UniProt 27–410 Author chain B； PDBConstruct 22–405； UniProt 27–410 Author chain C； PDBConstruct 22–405； 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	6nxg
Deposition date deposition_date	2019-02-08
Structure title title	Crystal structure of glycylpeptide N-tetradecanoyltransferase from Plasmodium vivax in complex with inhibitor 303a
Keywords keywords	;TRANSFERASE, Structural Genomics, Seattle Structural Genomics Center for Infectious Disease, SSGCID, transferase-transferase inhibitor complex ;; transferase/transferase inhibitor
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.

6nxg__assembly_2__model_1

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

Download this curve (.dat)

6nxg__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6nxg__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	22.66 Å
Rg (electron density)	21.29 Å
Total Rg	22.38 Å
Atom count	3274
Residues	385
Excluded volume	58850 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6nxg__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`6nxg__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`6nxg__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	47250.9 kDa
EC 编号 ec_number	2.3.1.97
Mutation mutation	27-410
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	11688

MGSSHHHHHHSAALEVLFQGPDYKFWYTQPVPKINDEFNESVNEPFISDNKVEDVRKDEYKLPPGYSWYVCDVKDEKDRSEIYTLLTDNYVEDDDNIFRFNYSAEFLLWALTSPNYLKTWHIGVKYDASNKLIGFISAIPTDICIHKRTIKMAEVNFLCVHKTLRSKRLAPVLIKEITRRINLENIWQAIYTAGVYLPKPVSDARYYHRSINVKKLIEIGFSSLNSRLTMSRAIKLYRVEDTLNIKNMRLMKKKDVEGVHKLLGSYLEQFNLYAVFTKEEIAHWFLPIENVIYTYVNEENGKIKDMISFYSLPSQILGNDKYSTLNAAYSFYNVTTTATFKQLMQDAILLAKRNNFDVFNALEVMQNKSVFEDLKFGEGDGSLKYYLYNWKCASFAPAHVGIVLL

Source Source

Source organism organism	Plasmodium vivax (strain Salvador I)
NCBI taxonomy ID ncbi_taxonomy_id	126793
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

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

Entity 3 Entity 3 non-polymer

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

Entity 4 Entity 4 non-polymer

Description description	OXAMIC ACID
Molecular weight formula_weight	89.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	5-(4-chlorophenyl)-3-({[3-(morpholine-4-carbonyl)phenyl]amino}methyl)pyridin-2(1H)-one
Molecular weight formula_weight	423.9 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 non-polymer

Description description	TETRADECANOYL-COA
Molecular weight formula_weight	977.9 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 7 Entity 7 non-polymer

Description description	BETA-MERCAPTOETHANOL
Molecular weight formula_weight	78.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 8 Entity 8 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 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	1687

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6. Fold Classification (SCOP + CATH) 11 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d6nxga1
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	d6nxga2
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	d6nxga3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d6nxgb1
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	d6nxgb2
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	d6nxgb3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d6nxgc1
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	d6nxgc2
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 (3 domains)

Domain ID domain_id	6nxgA00
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	6nxgB00
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	6nxgC00
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	57.420 Å
Unit-cell length b length_b	119.030 Å
Unit-cell length c length_c	175.350 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	1.600 Å
Low-resolution limit resolution_low	49.290 Å
R factor r_factor	0.1504
R_work r_work	0.1491
R_free r_free	0.1741

Crystal structure of glycylpeptide N-tetradecanoyltransferase from Plasmodium vivax in complex with inhibitor 303a

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

6nxg__assembly_2__model_1

6nxg__assembly_2__model_1 | I(q)

6nxg__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 (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

6. Fold Classification (SCOP + CATH) 11 domains

SCOP 2.08 (8 domains)

CATH v4.4 (3 domains)

7. Citations (1)

Crystal structure of glycylpeptide N-tetradecanoyltransferase from Plasmodium vivax in complex with inhibitor 303a

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

6nxg__assembly_2__model_1

6nxg__assembly_2__model_1 | I(q)

6nxg__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 (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

6. Fold Classification (SCOP + CATH) 11 domains

SCOP 2.08 (8 domains)

CATH v4.4 (3 domains)

7. Citations (1)