8Q24: HsNMT1

Name: PDB 8Q24: HsNMT1 in complex with both MyrCoA and (DAB)SFSKPR inhibitor peptide
Published: 2024-08-14
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: transferase

HsNMT1 in complex with both MyrCoA and (DAB)SFSKPR inhibitor peptide. Determined by X-ray diffraction at 1.9 Å resolution. Released 14 Aug 2024.

Method: X-ray diffraction
Resolution: 1.9 Å
Organism: Homo sapiens
Chains: 4
Atoms: 7,129
Mol. weight: 97.06 kDa
Ligands: MYA
Released: 14 Aug 2024

Explore 8Q24 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8Q24 contains 36 α-helices and 52 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, 25 β-strands

Element	Residues	Length	Sheet
α-helix	111-114	4
α-helix	120-122	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	183	1	4
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	314-315	2
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	415-416	2	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	5
β-strand	471-479	9	2
β-strand	482	1	1
α-helix	488-490	3
β-strand	491	1	2

Chain B: 18 helices, 24 β-strands

Element	Residues	Length	Sheet
α-helix	109-114	6
α-helix	120-122	3
β-strand	136	1	6
α-helix	140-142	3
α-helix	149-153	5
β-strand	156-160	5	7
α-helix	166-179	14
β-strand	182	1	8
β-strand	188-190	3	8
α-helix	194-201	8
α-helix	208-210	3
β-strand	211-216	6	7
β-strand	222-235	14	7
β-strand	238-250	13	7
α-helix	252-254	3
α-helix	259-272	14
β-strand	279-283	5	7
β-strand	292-300	9	7
α-helix	303-308	6
α-helix	314-315	2
α-helix	320-326	7
β-strand	338-340	3	7
α-helix	343-345	3
α-helix	346-357	12
β-strand	362-364	3	7
α-helix	368-375	8
β-strand	378	1	7
β-strand	382-388	7	7
β-strand	394-402	9	7
β-strand	405-407	3	8
β-strand	415-416	2	8
β-strand	418-421	4	7
β-strand	425	1	7
α-helix	431-444	14
β-strand	449-453	5	7
α-helix	458-460	3
β-strand	468-469	2	7
β-strand	470	1	9
β-strand	471-479	9	7
β-strand	482	1	6
α-helix	488-490	3
β-strand	491	1	7

Chain C: 0 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	4
β-strand	7	1	5

Chain E: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	7	1	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Glycylpeptide N-tetradecanoyltransferase 1	A, B	protein	402	Homo sapiens	P30419 (AlphaFold model)
Dab-ser-phe-ser-lys-pro-arg	C, E	protein	7	Homo sapiens

Sequence of entity 1 (A, B), FASTA

>8Q24_1 Glycylpeptide N-tetradecanoyltransferase 1 (chains A, B)
GGSEFSVGQGPAKTMEEASKRSYQFWDTQPVPKLGEVVNTHGPVEPDKDNIRQEPYTLPQ
GFTWDALDLGDRGVLKELYTLLNENYVEDDDNMFRFDYSPEFLLWALRPPGWLPQWHCGV
RVVSSRKLVGFISAIPANIHIYDTEKKMVEINFLCVHKKLRSKRVAPVLIREITRRVHLE
GIFQAVYTAGVVLPKPVGTCRYWHRSLNPRKLIEVKFSHLSRNMTMQRTMKLYRLPETPK
TAGLRPMETKDIPVVHQLLTRYLKQFHLTPVMSQEEVEHWFYPQENIIDTFVVENANGEV
TDFLSFYTLPSTIMNHPTHKSLKAAYSFYNVHTQTPLLDLMSDALVLAKMKGFDVFNALD
LMENKTFLEKLKFGIGDGNLQYYLYNWKCPSMGAEKVGLVLQ

Sequence of entity 2 (C, E), FASTA

>8Q24_2 DAB-SER-PHE-SER-LYS-PRO-ARG (chains C, E)
ASFSKPR

Ligands and cofactors

ID	Name	Formula	Copies
MYA	Tetradecanoyl-CoA	C35 H62 N7 O17 P3 S	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…
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

Browse structure collections

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