SMTL ID : 5mu6.1 (1 other biounit)

Human N-myristoyltransferase (NMT1) with Myristoyl-CoA and IMP-1088 inhibitor bound

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.88 Å

Oligo State

monomer

Ligands

1 x MYA: TETRADECANOYL-COA(Non-covalent)

MYA.1: 30 residues within 4Å: Chain A: Y.12, Q.13, F.14, W.15, N.74, Y.75, V.76, I.140, N.141, F.142, L.143, C.144, V.145, R.150, S.151, K.152, R.153, V.154, A.155, P.156, T.163, V.166, F.172, Q.173, A.174, Y.176, T.177, L.182, Y.374 Ligands: MG.2 28 PLIP interactions: 28 interactions with chain A Hydrophobic interactions: A:W.15, A:W.15, A:Y.75, A:V.76, A:I.140, A:L.143, A:L.143, A:V.145, A:V.166, A:A.174, A:Y.176, A:Y.176 Hydrogen bonds: A:Q.13, A:F.14, A:W.15, A:Y.75, A:F.142, A:L.143, A:L.143, A:V.145, A:R.150, A:R.150, A:S.151, A:R.153, A:V.154, A:A.155 Salt bridges: A:R.153, A:R.153

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 7 residues within 4Å: Chain A: L.149, R.150, S.151, K.152, R.153, V.154 Ligands: MYA.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:L.149

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 8 residues within 4Å: Chain A: P.21, K.184, P.185, V.186, L.373, W.376, K.377, C.378 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:P.185, A:L.373, A:L.373, A:W.376, A:C.378 Water bridges: A:K.184 GOL.4: 8 residues within 4Å: Chain A: E.139, P.259, M.261, W.269, Y.318, V.389, L.390, Q.391 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.318, A:Y.318, A:Q.391, A:Q.391 Water bridges: A:W.269

1 x KFK: 1-[5-[3,4-bis(fluoranyl)-2-[2-(1,3,5-trimethylpyrazol-4-yl)ethoxy]phenyl]-1-methyl-indazol-3-yl]-~{N},~{N}-dimethyl-methanamine(Non-covalent)

KFK.5: 20 residues within 4Å: Chain A: V.76, D.78, F.83, R.84, F.85, Y.87, N.141, T.177, G.179, Y.191, H.193, F.206, S.300, Y.315, N.346, A.347, L.348, L.369, L.390, Q.391 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.85, A:Y.191, A:F.206, A:L.348 Hydrogen bonds: A:S.300 Water bridges: A:N.141 pi-Stacking: A:F.85, A:Y.315

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mousnier, A. et al., Fragment-derived inhibitors of human N-myristoyltransferase block capsid assembly and replication of the common cold virus. Nat Chem (2018)

Release Date

2018-02-14

Peptides

Glycylpeptide N-tetradecanoyltransferase 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Glycylpeptide N-tetradecanoyltransferase 1

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