6skj

DeltaC2 C-terminal truncation of HsNMT1 in complex with MyrCoA and GNCFSKPR substrates

Method: X-RAY DIFFRACTION

▼

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

Glycylpeptide N-tetradecanoyltransferase 1

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Apoptosis-inducing factor 3 × 1 （Q96NN9） GLYCEROL × 1 TETRADECANOYL-COA × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Apoptosis-inducing factor 3 × 1 （Q96NN9） GLYCEROL × 2 COENZYME A × 1 MAGNESIUM ION × 1 TETRADECANOYL-COA × 1 MYRISTIC ACID × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NMT1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–400； UniProt 99–494 Author chain B； PDBConstruct 5–400； UniProt 99–494

Apoptosis-inducing factor 3

OrganismNot specified

UniProt Q96NN9

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Glycylpeptide N-tetradecanoyltransferase 1 × 1 （P30419） GLYCEROL × 1 TETRADECANOYL-COA × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Glycylpeptide N-tetradecanoyltransferase 1 × 1 （P30419） GLYCEROL × 2 COENZYME A × 1 MAGNESIUM ION × 1 TETRADECANOYL-COA × 1 MYRISTIC ACID × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	AIFM3_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–8； UniProt 2–9 Author chain D； PDBConstruct 1–8； UniProt 2–9

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	6skj
Deposition date deposition_date	2019-08-15
Structure title title	DeltaC2 C-terminal truncation of HsNMT1 in complex with MyrCoA and GNCFSKPR substrates
Keywords keywords	NMT, MYRISTOYLTRANSFERASE TYPE1, ACYLTRANSFERASE, GNAT, GCN5-RELATED N-ACETYLTRANSFERASES, TRANSFERASE; TRANSFERASE
Experimental Method method	X-RAY DIFFRACTION

▼

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.

6skj__assembly_2__model_1

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

Download this curve (.dat)

6skj__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6skj__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	22.43 Å
Rg (electron density)	21.08 Å
Total Rg	22.14 Å
Atom count	3268
Residues	398
Excluded volume	58558 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6skj__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`6skj__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Description description	Glycylpeptide N-tetradecanoyltransferase 1
Molecular weight formula_weight	46224.1 kDa
EC 编号 ec_number	2.3.1.97
Mutation mutation	L495stop
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	6773

GGSEFSVGQGPAKTMEEASKRSYQFWDTQPVPKLGEVVNTHGPVEPDKDNIRQEPYTLPQGFTWDALDLGDRGVLKELYTLLNENYVEDDDNMFRFDYSPEFLLWALRPPGWLPQWHCGVRVVSSRKLVGFISAIPANIHIYDTEKKMVEINFLCVHKKLRSKRVAPVLIREITRRVHLEGIFQAVYTAGVVLPKPVGTCRYWHRSLNPRKLIEVKFSHLSRNMTMQRTMKLYRLPETPKTAGLRPMETKDIPVVHQLLTRYLKQFHLTPVMSQEEVEHWFYPQENIIDTFVVENANGEVTDFLSFYTLPSTIMNHPTHKSLKAAYSFYNVHTQTPLLDLMSDALVLAKMKGFDVFNALDLMENKTFLEKLKFGIGDGNLQYYLYNWKCPSMGAEKVGLV

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Apoptosis-inducing factor 3
Molecular weight formula_weight	910.1 kDa
EC 编号 ec_number	1.-.-.-
Mutation mutation	G3N, P8R
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D

GNCFSKPR

Entity 3 Entity 3 non-polymer

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

Entity 4 Entity 4 non-polymer

Description description	COENZYME A
Molecular weight formula_weight	767.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

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

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	2

Entity 7 Entity 7 non-polymer

Description description	MYRISTIC ACID
Molecular weight formula_weight	228.4 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	90

▼

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	6skjA00
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	6skjB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	630 — Aminopeptidase
Homologous superfamily homologous superfamily	170 —

▶

Unit-cell length a length_a	92.965 Å
Unit-cell length b length_b	58.270 Å
Unit-cell length c length_c	154.132 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.92 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

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

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	49.371 Å
R factor r_factor	0.1906
R_work r_work	0.1890
R_free r_free	0.2188

DeltaC2 C-terminal truncation of HsNMT1 in complex with MyrCoA and GNCFSKPR substrates

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

Glycylpeptide N-tetradecanoyltransferase 1

State in the Current Structure

Other States of the Same Protein in the Database

Apoptosis-inducing factor 3

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

6skj__assembly_2__model_1

6skj__assembly_2__model_1 | I(q)

6skj__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 polymer

Polymer 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) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

DeltaC2 C-terminal truncation of HsNMT1 in complex with MyrCoA and GNCFSKPR substrates

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

Glycylpeptide N-tetradecanoyltransferase 1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Apoptosis-inducing factor 3

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

6skj__assembly_2__model_1

6skj__assembly_2__model_1 | I(q)

6skj__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 polymer

Polymer 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) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)