8Q3S: HsNMT1

Name: PDB 8Q3S: HsNMT1 in complex with both MyrCoA and GNCFSKAR inhibitor peptide
Published: 2024-08-14
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: transferase

HsNMT1 in complex with both MyrCoA and GNCFSKAR inhibitor peptide. Determined by X-ray diffraction at 1.78 Å resolution. Released 14 Aug 2024.

Method: X-ray diffraction
Resolution: 1.78 Å
Organisms: Homo sapiens, unidentified
Chains: 4
Atoms: 7,306
Mol. weight: 97.02 kDa
Ligands: COA, MYR
Released: 14 Aug 2024

Explore 8Q3S in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8Q3S contains 35 α-helices and 50 β-strands across 4 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: 18 helices, 24 β-strands

Element	Residues	Length	Sheet
α-helix	109-113	5
α-helix	120-122	3
α-helix	130-132	3
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	259-272	14
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	362-364	3	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	416	1	3
β-strand	418-421	4	2
β-strand	425-426	2	2
α-helix	431-444	14
β-strand	449-453	5	2
α-helix	458-460	3
β-strand	468-469	2	2
β-strand	470	1	4
β-strand	471-479	9	2
β-strand	482	1	1
α-helix	488-490	3
β-strand	491	1	2

Chain B: 17 helices, 24 β-strands

Element	Residues	Length	Sheet
α-helix	109-113	5
α-helix	120-122	3
β-strand	136	1	5
α-helix	140-142	3
α-helix	149-153	5
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	259-272	14
β-strand	279-283	5	6
β-strand	292-300	9	6
α-helix	303-308	6
α-helix	320-327	8
β-strand	338-340	3	6
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	6
β-strand	382-388	7	6
β-strand	394-402	9	6
β-strand	405-407	3	7
β-strand	415-416	2	7
β-strand	418-421	4	6
β-strand	425-426	2	6
α-helix	431-444	14
β-strand	449-453	5	6
α-helix	459-462	4
β-strand	468-469	2	6
β-strand	470	1	8
β-strand	471-479	9	6
β-strand	482	1	5
α-helix	488-490	3
β-strand	491	1	6

Chains C and D: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	8	1	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Glycylpeptide N-tetradecanoyltransferase 1	A, B	protein	401	Homo sapiens	P30419 (AlphaFold model)
Gly-asn-cys-phe-ser-lys-ala-arg	C, D	protein	8	unidentified

Sequence of entity 1 (A, B), FASTA

>8Q3S_1 Glycylpeptide N-tetradecanoyltransferase 1 (chains A, B)
GSEFSVGQGPAKTMEEASKRSYQFWDTQPVPKLGEVVNTHGPVEPDKDNIRQEPYTLPQG
FTWDALDLGDRGVLKELYTLLNENYVEDDDNMFRFDYSPEFLLWALRPPGWLPQWHCGVR
VVSSRKLVGFISAIPANIHIYDTEKKMVEINFLCVHKKLRSKRVAPVLIREITRRVHLEG
IFQAVYTAGVVLPKPVGTCRYWHRSLNPRKLIEVKFSHLSRNMTMQRTMKLYRLPETPKT
AGLRPMETKDIPVVHQLLTRYLKQFHLTPVMSQEEVEHWFYPQENIIDTFVVENANGEVT
DFLSFYTLPSTIMNHPTHKSLKAAYSFYNVHTQTPLLDLMSDALVLAKMKGFDVFNALDL
MENKTFLEKLKFGIGDGNLQYYLYNWKCPSMGAEKVGLVLQ

Sequence of entity 2 (C, D), FASTA

>8Q3S_2 GLY-ASN-CYS-PHE-SER-LYS-ALA-ARG (chains C, D)
GNCFSKAR

Ligands and cofactors

ID	Name	Formula	Copies
COA	Coenzyme a	C21 H36 N7 O16 P3 S	2
MYR	Myristic acid	C14 H28 O2	2

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

Primary citation

Novel, tightly structurally related N-myristoyltransferase inhibitors display equally potent yet distinct inhibitory mechanisms. Riviere, F., Dian, C., Dutheil, R.F. et al. Structure (2024) 32:1737-1750.e3. DOI 10.1016/j.str.2024.08.001 · 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…
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…
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 8Q3S 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.