5O6H: Human NMT1

Name: PDB 5O6H: Human NMT1 in complex with myristoyl-CoA and inhibitor IMP-917
Published: 2018-05-16
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: transferase

Human NMT1 in complex with myristoyl-CoA and inhibitor IMP-917. Determined by X-ray diffraction at 1.29 Å resolution. Released 16 May 2018.

Method: X-ray diffraction
Resolution: 1.29 Å
Organism: Homo sapiens
Chains: 2
Atoms: 7,829
Mol. weight: 94.87 kDa
Ligands: MG, 9M2, PO4, MYA
Released: 16 May 2018

Explore 5O6H in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5O6H contains 36 α-helices and 44 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, 22 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	260-272	13
β-strand	279-283	5	2
β-strand	292-300	9	2
α-helix	303-308	6
α-helix	320-327	8
β-strand	338-340	3	2
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	2
β-strand	382-388	7	2
β-strand	394-402	9	2
β-strand	405-407	3	3
β-strand	415-416	2	3
β-strand	418-421	4	2
β-strand	425	1	2
α-helix	431-444	14
β-strand	449-453	5	2
α-helix	458-460	3
β-strand	468-479	12	2
β-strand	482	1	1
α-helix	488-490	3
β-strand	491	1	2

Chain B: 19 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	120-122	3
α-helix	126-127	2
β-strand	136	1	4
α-helix	140-142	3
α-helix	149-152	4
β-strand	156-160	5	5
α-helix	166-179	14
β-strand	182	1	6
β-strand	188-190	3	6
α-helix	194-201	8
α-helix	208-210	3
β-strand	211-216	6	5
β-strand	222-235	14	5
β-strand	238-250	13	5
α-helix	252-254	3
α-helix	259-272	14
β-strand	279-283	5	5
β-strand	292-300	9	5
α-helix	303-308	6
α-helix	314-315	2
α-helix	320-327	8
β-strand	338-340	3	5
α-helix	343-345	3
α-helix	346-357	12
β-strand	362-365	4	5
α-helix	368-375	8
β-strand	378	1	5
β-strand	382-388	7	5
β-strand	394-402	9	5
β-strand	405-407	3	6
α-helix	414-415	2
β-strand	416	1	6
β-strand	418-421	4	5
β-strand	425-426	2	5
α-helix	431-444	14
β-strand	449-453	5	5
α-helix	458-460	3
β-strand	468-479	12	5
β-strand	482	1	4
α-helix	488-490	3
β-strand	491	1	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Glycylpeptide N-tetradecanoyltransferase 1	A, B	protein	391	Homo sapiens	P30419 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5O6H_1 Glycylpeptide N-tetradecanoyltransferase 1 (chains A, B)
GPHMEEASKRSYQFWDTQPVPKLGEVVNTHGPVEPDKDNIRQEPYTLPQGFTWDALDLGD
RGVLKELYTLLNENYVEDDDNMFRFDYSPEFLLWALRPPGWLPQWHCGVRVVSSRKLVGF
ISAIPANIHIYDTEKKMVEINFLCVHKKLRSKRVAPVLIREITRRVHLEGIFQAVYTAGV
VLPKPVGTCRYWHRSLNPRKLIEVKFSHLSRNMTMQRTMKLYRLPETPKTAGLRPMETKD
IPVVHQLLTRYLKQFHLTPVMSQEEVEHWFYPQENIIDTFVVENANGEVTDFLSFYTLPS
TIMNHPTHKSLKAAYSFYNVHTQTPLLDLMSDALVLAKMKGFDVFNALDLMENKTFLEKL
KFGIGDGNLQYYLYNWKCPSMGAEKVGLVLQ

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	2
9M2	1-[5-[4-fluoranyl-2-[2-(1,3,5-trimethylpyrazol-4-yl)ethoxy]phenyl]-2~{H}-indazo…	C24 H28 F N5 O	2
PO4	Phosphate ion	O4 P	8
MYA	Tetradecanoyl-CoA	C35 H62 N7 O17 P3 S	2

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

Primary citation

Fragment-derived inhibitors of human N-myristoyltransferase block capsid assembly and replication of the common cold virus. Mousnier, A., Bell, A.S., Swieboda, D.P. et al. Nat Chem (2018) 10:599-606. DOI 10.1038/s41557-018-0039-2 · PubMed

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

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…
4C2Y 1.64 Å, Human N-myristoyltransferase (NMT1) with Myristoyl-CoA co-factor
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

About this viewer

MolViewer shows 5O6H directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.