4C2Y: Glycylpeptide N-tetradecanoyltransferase 1

Name: PDB 4C2Y: Human N-myristoyltransferase (NMT1) with Myristoyl-CoA co-factor
Published: 2014-10-01
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: transferase

Human N-myristoyltransferase (NMT1) with Myristoyl-CoA co-factor. Determined by X-ray diffraction at 1.64 Å resolution. Released 1 Oct 2014.

Method: X-ray diffraction
Resolution: 1.64 Å
Organism: HOMO SAPIENS
Chains: 2
Atoms: 7,569
Mol. weight: 98.24 kDa
Ligands: MYA, MG, CIT
Released: 1 Oct 2014

Explore 4C2Y in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4C2Y contains 36 α-helices and 49 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 17 helices, 25 β-strands

Element	Residues	Length	Sheet
α-helix	120-122	3
α-helix	126-127	2
β-strand	136	1	1
α-helix	140-142	3
α-helix	149-153	5
β-strand	156-160	5	2
α-helix	166-179	14
β-strand	182	1	3
β-strand	188-190	3	3
α-helix	194-201	8
α-helix	208-210	3
β-strand	211-216	6	2
β-strand	222-235	14	2
β-strand	238-250	13	2
α-helix	252-254	3
α-helix	259-273	15
β-strand	279-283	5	2
β-strand	292-294	3	2
β-strand	296-300	5	4
α-helix	303-308	6
α-helix	320-327	8
β-strand	338-340	3	4
α-helix	343-345	3
α-helix	346-357	12
β-strand	362-365	4	2
α-helix	368-375	8
β-strand	378	1	4
β-strand	382-388	7	4
β-strand	394-402	9	4
β-strand	405-407	3	3
β-strand	415-416	2	3
β-strand	418-421	4	4
β-strand	425	1	4
α-helix	431-444	14
β-strand	449-453	5	4
α-helix	458-460	3
β-strand	468-469	2	4
β-strand	474-479	6	2
β-strand	482	1	1
β-strand	486	1	2
α-helix	488-490	3
β-strand	491	1	2

Chain B: 19 helices, 24 β-strands

Element	Residues	Length	Sheet
α-helix	120-122	3
α-helix	126-127	2
β-strand	136	1	5
α-helix	140-142	3
α-helix	149-152	4
β-strand	156-160	5	6
α-helix	166-179	14
β-strand	182	1	7
β-strand	188-190	3	7
α-helix	194-201	8
α-helix	208-210	3
β-strand	211-216	6	6
β-strand	222-235	14	6
β-strand	238-250	13	6
α-helix	252-254	3
α-helix	259-273	15
β-strand	279-283	5	6
β-strand	292-294	3	6
β-strand	296-300	5	8
α-helix	303-308	6
α-helix	314-315	2
α-helix	320-326	7
β-strand	338-340	3	8
α-helix	343-345	3
α-helix	346-357	12
β-strand	362-365	4	6
α-helix	368-375	8
β-strand	378	1	8
β-strand	382-388	7	8
β-strand	394-402	9	8
β-strand	405-407	3	7
α-helix	414-415	2
β-strand	416	1	7
β-strand	418-421	4	8
β-strand	425-426	2	8
α-helix	431-444	14
β-strand	449-453	5	8
α-helix	458-460	3
β-strand	468-469	2	8
β-strand	474-479	6	6
β-strand	482	1	5
α-helix	488-490	3
β-strand	491	1	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Glycylpeptide N-tetradecanoyltransferase 1	A, B	protein	410	HOMO SAPIENS	P30419 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>4C2Y_1 GLYCYLPEPTIDE N-TETRADECANOYLTRANSFERASE 1 (chains A, B)
MGSSHHHHHHSSGLEVLFQGPHMEEASKRSYQFWDTQPVPKLGEVVNTHGPVEPDKDNIR
QEPYTLPQGFTWDALDLGDRGVLKELYTLLNENYVEDDDNMFRFDYSPEFLLWALRPPGW
LPQWHCGVRVVSSRKLVGFISAIPANIHIYDTEKKMVEINFLCVHKKLRSKRVAPVLIRE
ITRRVHLEGIFQAVYTAGVVLPKPVGTCRYWHRSLNPRKLIEVKFSHLSRNMTMQRTMKL
YRLPETPKTAGLRPMETKDIPVVHQLLTRYLKQFHLTPVMSQEEVEHWFYPQENIIDTFV
VENANGEVTDFLSFYTLPSTIMNHPTHKSLKAAYSFYNVHTQTPLLDLMSDALVLAKMKG
FDVFNALDLMENKTFLEKLKFGIGDGNLQYYLYNWKCPSMGAEKVGLVLQ

Ligands and cofactors

ID	Name	Formula	Copies
MYA	Tetradecanoyl-CoA	C35 H62 N7 O17 P3 S	2
MG	Magnesium ion	Mg	2
CIT	Citric acid	C6 H8 O7	2

Water and common crystallization additives (GOL) are not listed.

Primary citation

Global Profiling of Co- and Post-Translationally N-Myristoylated Proteomes in Human Cells. Thinon, E., Serwa, R.A., Broncel, M. et al. Nat Commun (2014) 5:4919. DOI 10.1038/NCOMMS5919 · PubMed

Other PDB entries of the same protein (UniProt P30419 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5O6H 1.29 Å, Human NMT1 in complex with myristoyl-CoA and inhibitor IMP-917
3IU1 1.42 Å, Crystal Structure of human type-I N-myristoyltransferase with bound myristoyl-CoA
5O6J 1.45 Å, Human NMT1 in complex with myristoyl-CoA and inhibitor IMP-1031
7OWM 1.5 Å, HsNMT1 in complex with both MyrCoA and HCPA substrate peptide GKQNSKLR
3JTK 1.61 Å, Crystal Structure of human type-I N-myristoyltransferase with bound myristoyl-CoA and…
7OWO 1.7 Å, HsNMT1 in complex with both MyrCoA and N-acetylated KSFSKPR peptide
3IU2 1.73 Å, Crystal Structure of human type-I N-myristoyltransferase with bound myristoyl-CoA and…
8Q3S 1.78 Å, HsNMT1 in complex with both MyrCoA and GNCFSKAR inhibitor peptide
3IWE 1.79 Å, Crystal Structure of human type-I N-myristoyltransferase with bound myristoyl-CoA and…
7OWP 1.81 Å, HsNMT1 in complex with both MyrCoA and ACE-G-(L-ORN)SFSKPR
5O9U 1.85 Å, HsNMT1 in complex with CoA and Myristoylated-GCSVSKKK octapeptide
6SK8 1.87 Å, DeltaC3 C-terminal truncation of HsNMT1 in complex with MyrCoA and GDCFSKPR substrates

Browse structure collections

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