6SK2: HsNMT1

Name: PDB 6SK2: HsNMT1 in complex with both MyrCoA and Acetylated-GKSFSKPR peptide reveals N-terminal Lysine Myristoylation
Published: 2020-03-18
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: transferase

HsNMT1 in complex with both MyrCoA and Acetylated-GKSFSKPR peptide reveals N-terminal Lysine Myristoylation. Determined by X-ray diffraction at 1.9 Å resolution. Released 18 Mar 2020.

Method: X-ray diffraction
Resolution: 1.9 Å
Organism: Homo sapiens
Chains: 4
Atoms: 7,411
Mol. weight: 97.05 kDa
Ligands: COA, MYR, MYA
Released: 18 Mar 2020

Explore 6SK2 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6SK2 contains 34 α-helices and 53 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: 17 helices, 25 β-strands

Element	Residues	Length	Sheet
α-helix	109-112	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	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	1	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: 17 helices, 25 β-strands

Element	Residues	Length	Sheet
α-helix	109-112	4
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	292-294	3	7
β-strand	296-300	5	9
α-helix	303-308	6
α-helix	320-327	8
β-strand	338-340	3	9
α-helix	343-345	3
α-helix	346-357	12
β-strand	362-365	4	7
α-helix	368-375	8
β-strand	378	1	9
β-strand	382-388	7	9
β-strand	394-402	9	9
β-strand	405-407	3	8
β-strand	415-416	2	8
β-strand	418-421	4	9
β-strand	425-426	2	9
α-helix	431-444	14
β-strand	449-453	5	9
α-helix	458-460	3
β-strand	468-469	2	9
β-strand	470	1	10
β-strand	474-479	6	7
β-strand	482	1	6
α-helix	488-490	3
β-strand	491	1	7

Chain D: 0 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	4
β-strand	8	1	5

Chain F: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	8	1	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Glycylpeptide N-tetradecanoyltransferase 1	A, B	protein	402	Homo sapiens	P30419 (AlphaFold model)
Apoptosis-inducing factor 3	D, F	protein	9	Homo sapiens	Q96NN9 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>6SK2_1 Glycylpeptide N-tetradecanoyltransferase 1 (chains A, B)
GGSEFSVGQGPAKTMEEASKRSYQFWDTQPVPKLGEVVNTHGPVEPDKDNIRQEPYTLPQ
GFTWDALDLGDRGVLKELYTLLNENYVEDDDNMFRFDYSPEFLLWALRPPGWLPQWHCGV
RVVSSRKLVGFISAIPANIHIYDTEKKMVEINFLCVHKKLRSKRVAPVLIREITRRVHLE
GIFQAVYTAGVVLPKPVGTCRYWHRSLNPRKLIEVKFSHLSRNMTMQRTMKLYRLPETPK
TAGLRPMETKDIPVVHQLLTRYLKQFHLTPVMSQEEVEHWFYPQENIIDTFVVENANGEV
TDFLSFYTLPSTIMNHPTHKSLKAAYSFYNVHTQTPLLDLMSDALVLAKMKGFDVFNALD
LMENKTFLEKLKFGIGDGNLQYYLYNWKCPSMGAEKVGLVLQ

Sequence of entity 2 (D, F), FASTA

>6SK2_2 Apoptosis-inducing factor 3 (chains D, F)
XGKSFSKPR

Ligands and cofactors

ID	Name	Formula	Copies
COA	Coenzyme a	C21 H36 N7 O16 P3 S	1
MYR	Myristic acid	C14 H28 O2	1
MYA	Tetradecanoyl-CoA	C35 H62 N7 O17 P3 S	1

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

Primary citation

High-resolution snapshots of human N-myristoyltransferase in action illuminate a mechanism promoting N-terminal Lys and Gly myristoylation. Dian, C., Perez-Dorado, I., Riviere, F. et al. Nat Commun (2020) 11:1132-1132. DOI 10.1038/s41467-020-14847-3 · 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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