SMTL ID : 7owo.1 (1 other biounit)

HsNMT1 in complex with both MyrCoA and N-acetylated KSFSKPR peptide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

monomer

Ligands

1 x ACE- LYS- SER- PHE- SER- LYS- PRO- ARG: N-Acetyl-LYS-SER-PHE-SER-LYS-PRO-ARG(Non-covalent)

ACE-LYS-SER-PHE-SER-LYS-PRO-ARG.1: 28 residues within 4Å: Chain A: Y.86, V.87, E.88, D.89, D.90, D.91, F.94, F.96, Y.98, N.152, T.188, G.190, Y.202, H.204, F.217, H.219, Y.307, S.311, Y.326, I.375, G.376, D.377, G.378, N.379, L.380, Q.402 Ligands: MYA.4, MYR.5 28 PLIP interactions: 28 interactions with chain A Hydrophobic interactions: A:D.89, A:F.94, A:F.96, A:F.217, A:Y.326 Hydrogen bonds: A:D.89, A:D.90, A:D.91, A:Y.98, A:Y.98, A:T.188, A:Y.202, A:Y.202, A:I.375, A:D.377, A:D.377, A:D.377, A:D.377, A:G.378, A:N.379 Water bridges: A:D.90, A:N.152, A:T.188, A:G.190, A:Y.326, A:Y.326, A:N.379 Salt bridges: A:H.219

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 10 residues within 4Å: Chain A: P.32, K.195, P.196, V.197, Y.383, L.384, W.387, K.388, C.389, S.391 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:P.196, A:L.384, A:L.384, A:C.389, A:C.389 Water bridges: A:K.195

1 x COA: COENZYME A(Non-covalent)

COA.3: 26 residues within 4Å: Chain A: R.21, S.22, Y.23, Q.24, F.25, W.26, N.85, Y.86, V.87, L.154, C.155, V.156, R.161, S.162, K.163, R.164, V.165, A.166, P.167, I.170, A.189, G.190, V.191, L.193 Ligands: MYA.4, MYR.5 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:Y.86, A:V.87, A:L.154, A:V.156 Hydrogen bonds: A:Q.24, A:F.25, A:W.26, A:V.156, A:R.161, A:S.162, A:R.164, A:V.165, A:A.166 Water bridges: A:R.21, A:R.21, A:K.163, A:K.163 Salt bridges: A:R.21

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

MYA.4: 36 residues within 4Å: Chain A: R.21, Y.23, Q.24, F.25, W.26, N.85, Y.86, V.87, I.151, N.152, F.153, L.154, C.155, V.156, R.161, S.162, K.163, R.164, V.165, A.166, P.167, I.170, T.174, V.177, H.178, I.182, F.183, Q.184, A.185, Y.187, T.188, L.193, Y.385 Ligands: ACE-LYS-SER-PHE-SER-LYS-PRO-ARG.1, COA.3, MYR.5 31 PLIP interactions: 31 interactions with chain A Hydrophobic interactions: A:Y.86, A:V.87, A:I.151, A:L.154, A:L.154, A:V.156, A:I.170, A:V.177, A:A.185, A:Y.187, A:Y.187, A:Y.385 Hydrogen bonds: A:R.21, A:Q.24, A:F.25, A:W.26, A:Y.86, A:F.153, A:L.154, A:L.154, A:V.156, A:R.161, A:R.161, A:S.162, A:R.164, A:V.165, A:A.166 Water bridges: A:R.21, A:K.163, A:K.163 Salt bridges: A:R.21

1 x MYR: MYRISTIC ACID(Non-covalent)

MYR.5: 20 residues within 4Å: Chain A: W.26, Y.86, I.151, N.152, F.153, L.154, I.170, T.174, V.177, H.178, I.182, F.183, Q.184, A.185, Y.187, T.188, Y.385 Ligands: ACE-LYS-SER-PHE-SER-LYS-PRO-ARG.1, COA.3, MYA.4 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:I.151, A:L.154, A:I.170, A:V.177, A:A.185, A:Y.187, A:Y.187, A:Y.385 Hydrogen bonds: A:Y.86, A:L.154

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Riviere, F. et al., Structural and Large-scale Analysis Unveil the Intertwined Paths Promoting NMT-catalyzed Lysine and Glycine Myristoylation. J.Mol.Biol. (2022)

Release Date

2022-12-21

Peptides

Glycylpeptide N-tetradecanoyltransferase 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Glycylpeptide N-tetradecanoyltransferase 1

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