6FZ5: Glycylpeptide N-tetradecanoyltransferase 1

Name: PDB 6FZ5: Human N-myristoyltransferase (NMT1) with Myristoyl-CoA and inhibitor bound
Published: 2019-03-27
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: transferase

Human N-myristoyltransferase (NMT1) with Myristoyl-CoA and inhibitor bound. Determined by X-ray diffraction at 1.89 Å resolution. Released 27 Mar 2019.

Method: X-ray diffraction
Resolution: 1.89 Å
Organism: Homo sapiens
Chains: 2
Atoms: 6,731
Mol. weight: 92.37 kDa
Ligands: BXN, MYA, MG
Released: 27 Mar 2019

Explore 6FZ5 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6FZ5 contains 35 α-helices and 44 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: 17 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	120-122	3
α-helix	126-127	2
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	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	468-479	12	2
β-strand	482	1	1
α-helix	488-490	3
β-strand	491	1	2

Chain B: 18 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	120-122	3
α-helix	126-127	2
β-strand	136	1	4
α-helix	140-142	3
α-helix	149-153	5
β-strand	156-160	5	5
α-helix	166-179	14
β-strand	182	1	6
β-strand	188-190	3	6
α-helix	194-201	8
α-helix	208-210	3
β-strand	211-216	6	5
β-strand	222-235	14	5
β-strand	238-250	13	5
α-helix	252-254	3
α-helix	259-272	14
β-strand	279-283	5	5
β-strand	292-300	9	5
α-helix	303-308	6
α-helix	320-327	8
β-strand	338-340	3	5
α-helix	343-345	3
α-helix	346-356	11
α-helix	357-359	3
β-strand	362-364	3	5
α-helix	368-375	8
β-strand	378	1	5
β-strand	382-388	7	5
β-strand	394-402	9	5
β-strand	405-407	3	6
β-strand	415-416	2	6
β-strand	418-421	4	5
β-strand	425	1	5
α-helix	431-444	14
β-strand	449-453	5	5
α-helix	458-460	3
β-strand	468-479	12	5
β-strand	482	1	4
α-helix	488-490	3
β-strand	491	1	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Glycylpeptide N-tetradecanoyltransferase 1	A, B	protein	382	Homo sapiens	P30419 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>6FZ5_1 Glycylpeptide N-tetradecanoyltransferase 1 (chains A, B)
RSYQFWDTQPVPKLGEVVNTHGPVEPDKDNIRQEPYTLPQGFTWDALDLGDRGVLKELYT
LLNENYVEDDDNMFRFDYSPEFLLWALRPPGWLPQWHCGVRVVSSRKLVGFISAIPANIH
IYDTEKKMVEINFLCVHKKLRSKRVAPVLIREITRRVHLEGIFQAVYTAGVVLPKPVGTC
RYWHRSLNPRKLIEVKFSHLSRNMTMQRTMKLYRLPETPKTAGLRPMETKDIPVVHQLLT
RYLKQFHLTPVMSQEEVEHWFYPQENIIDTFVVENANGEVTDFLSFYTLPSTIMNHPTHK
SLKAAYSFYNVHTQTPLLDLMSDALVLAKMKGFDVFNALDLMENKTFLEKLKFGIGDGNL
QYYLYNWKCPSMGAEKVGLVLQ

Ligands and cofactors

ID	Name	Formula	Copies
BXN	4-[3-[(8~{a}~{R})-3,4,6,7,8,8~{a}-hexahydro-1~{H}-pyrrolo[1,2-a]pyrazin-2-yl]pr…	C23 H33 Cl2 N5 O2 S	2
MYA	Tetradecanoyl-CoA	C35 H62 N7 O17 P3 S	2
MG	Magnesium ion	Mg	2

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

Primary citation

How To Design Selective Ligands for Highly Conserved Binding Sites: A Case Study UsingN-Myristoyltransferases as a Model System. Kersten, C., Fleischer, E., Kehrein, J. et al. J Med Chem (2020) 63:2095-2113. DOI 10.1021/acs.jmedchem.9b00586 · 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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