7RK3: Human N-myristoyltransferase 1 fragment

Name: PDB 7RK3: Crystal structure of human N-myristoyltransferase 1 fragment (residues 109-496) bound to diacylated human Arf6 octapeptide and Coenzyme A
Published: 2022-07-27
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: transferase

Crystal structure of human N-myristoyltransferase 1 fragment (residues 109-496) bound to diacylated human Arf6 octapeptide and Coenzyme A. Determined by X-ray diffraction at 2.05 Å resolution. Released 27 Jul 2022.

Method: X-ray diffraction
Resolution: 2.05 Å
Organism: Homo sapiens
Chains: 2
Atoms: 3,513
Mol. weight: 47.13 kDa
Ligands: 6NA, MYR, 4PS
Released: 27 Jul 2022

Explore 7RK3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7RK3 contains 15 α-helices and 23 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: 15 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	149-153	5
β-strand	156-160	5	1
α-helix	166-179	14
β-strand	182	1	2
β-strand	188-190	3	2
α-helix	194-201	8
α-helix	208-210	3
β-strand	211-216	6	1
β-strand	222-235	14	1
β-strand	238-250	13	1
α-helix	252-254	3
α-helix	260-272	13
β-strand	279-283	5	1
β-strand	292-300	9	1
α-helix	303-308	6
α-helix	314-315	2
α-helix	320-326	7
β-strand	338-340	3	1
α-helix	343-345	3
α-helix	346-357	12
β-strand	362-365	4	1
α-helix	368-375	8
β-strand	378	1	1
β-strand	382-388	7	1
β-strand	394-402	9	1
β-strand	405-407	3	2
β-strand	415-416	2	2
β-strand	418-421	4	1
β-strand	425	1	1
α-helix	431-444	14
β-strand	449-453	5	1
α-helix	458-460	3
β-strand	468-469	2	1
β-strand	470	1	3
β-strand	471-479	9	1
α-helix	488-490	3
β-strand	491	1	1

Chain B: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	8	1	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Glycylpeptide N-tetradecanoyltransferase 1	A	protein	391	Homo sapiens	P30419 (AlphaFold model)
ADP-ribosylation factor 6	B	protein	8	Homo sapiens	P62330 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>7RK3_1 Glycylpeptide N-tetradecanoyltransferase 1 (chains A)
GPHMEEASKRSYQFWDTQPVPKLGEVVNTHGPVEPDKDNIRQEPYTLPQGFTWDALDLGD
RGVLKELYTLLNENYVEDDDNMFRFDYSPEFLLWALRPPGWLPQWHCGVRVVSSRKLVGF
ISAIPANIHIYDTEKKMVEINFLCVHKKLRSKRVAPVLIREITRRVHLEGIFQAVYTAGV
VLPKPVGTCRYWHRSLNPRKLIEVKFSHLSRNMTMQRTMKLYRLPETPKTAGLRPMETKD
IPVVHQLLTRYLKQFHLTPVMSQEEVEHWFYPQENIIDTFVVENANGEVTDFLSFYTLPS
TIMNHPTHKSLKAAYSFYNVHTQTPLLDLMSDALVLAKMKGFDVFNALDLMENKTFLEKL
KFGIGDGNLQYYLYNWKCPSMGAEKVGLVLQ

Sequence of entity 2 (B), FASTA

>7RK3_2 ADP-ribosylation factor 6 (chains B)
GKVLSKIF

Ligands and cofactors

ID	Name	Formula	Copies
6NA	Hexanoic acid	C6 H12 O2	1
MYR	Myristic acid	C14 H28 O2	1
4PS	4'-diphospho pantetheine	C11 H24 N2 O10 P2 S	1

Primary citation

Crystal structure of human N-myristoyltransferase 1 fragment (residues 109-496) bound to diacylated human Arf6 octapeptide and Coenzyme A. Fenwick, M.K., Lin, H. To be published.

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

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