6SKJ: DeltaC2 C-terminal truncation of HsNMT1

Name: PDB 6SKJ: DeltaC2 C-terminal truncation of HsNMT1 in complex with MyrCoA and GNCFSKPR substrates
Published: 2020-03-18
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: transferase

DeltaC2 C-terminal truncation of HsNMT1 in complex with MyrCoA and GNCFSKPR substrates. Determined by X-ray diffraction at 2.8 Å resolution. Released 18 Mar 2020.

Method: X-ray diffraction
Resolution: 2.8 Å
Organism: Homo sapiens
Chains: 4
Atoms: 6,773
Mol. weight: 97.52 kDa
Ligands: MYR, MYA, MG, COA
Released: 18 Mar 2020

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

Secondary structure: helices and β-sheets

6SKJ contains 36 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
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	320-326	7
β-strand	338-340	3	2
α-helix	343-345	3
α-helix	346-356	11
α-helix	357-359	3
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	456-460	5
β-strand	467-469	3	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: 18 helices, 24 β-strands

Element	Residues	Length	Sheet
α-helix	109-114	6
α-helix	120-122	3
α-helix	126-127	2
β-strand	136	1	5
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	362-364	3	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	458-460	3
α-helix	463-465	3
β-strand	467-469	3	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	400	Homo sapiens	P30419 (AlphaFold model)
Apoptosis-inducing factor 3	C, D	protein	8	Homo sapiens	Q96NN9 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>6SKJ_1 Glycylpeptide N-tetradecanoyltransferase 1 (chains A, B)
GGSEFSVGQGPAKTMEEASKRSYQFWDTQPVPKLGEVVNTHGPVEPDKDNIRQEPYTLPQ
GFTWDALDLGDRGVLKELYTLLNENYVEDDDNMFRFDYSPEFLLWALRPPGWLPQWHCGV
RVVSSRKLVGFISAIPANIHIYDTEKKMVEINFLCVHKKLRSKRVAPVLIREITRRVHLE
GIFQAVYTAGVVLPKPVGTCRYWHRSLNPRKLIEVKFSHLSRNMTMQRTMKLYRLPETPK
TAGLRPMETKDIPVVHQLLTRYLKQFHLTPVMSQEEVEHWFYPQENIIDTFVVENANGEV
TDFLSFYTLPSTIMNHPTHKSLKAAYSFYNVHTQTPLLDLMSDALVLAKMKGFDVFNALD
LMENKTFLEKLKFGIGDGNLQYYLYNWKCPSMGAEKVGLV

Sequence of entity 2 (C, D), FASTA

>6SKJ_2 Apoptosis-inducing factor 3 (chains C, D)
GNCFSKPR

Ligands and cofactors

ID	Name	Formula	Copies
MYR	Myristic acid	C14 H28 O2	1
MYA	Tetradecanoyl-CoA	C35 H62 N7 O17 P3 S	2
MG	Magnesium ion	Mg	1
COA	Coenzyme a	C21 H36 N7 O16 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

About this viewer

MolViewer shows 6SKJ 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.