SMTL ID : 7owu.2 (1 other biounit)

HsNMT1 in complex with both CoA and Myr-ANCFSKPR peptide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.08 Å

Oligo State

monomer

Ligands

1 x ALA- ASN- CYS- PHE- SER- LYS- PRO- ARG: ALA-ASN-CYS-PHE-SER-LYS-PRO-ARG(Non-covalent)

ALA-ASN-CYS-PHE-SER-LYS-PRO-ARG.1: 29 residues within 4Å: Chain A: Y.86, V.87, E.88, D.89, D.91, M.93, F.94, F.96, Y.98, N.152, T.188, A.189, G.190, R.201, Y.202, H.204, F.217, H.219, Y.307, S.311, I.375, G.376, D.377, G.378, N.379, L.380, Q.402 Ligands: COA.2, MYR.6 32 PLIP interactions: 32 interactions with chain A Hydrophobic interactions: A:V.87, A:D.89, A:F.94, A:F.94, A:F.94, A:F.96, A:F.96, A:F.217, A:I.375 Hydrogen bonds: A:Y.86, A:D.91, A:D.91, A:D.91, A:T.188, A:R.201, A:Y.202, A:Y.307, A:I.375, A:D.377, A:D.377, A:D.377, A:G.378, A:G.378, A:Q.402 Water bridges: A:Y.98, A:I.151, A:T.188, A:G.190, A:H.219, A:Y.326, A:D.377 Salt bridges: A:H.219

1 x COA: COENZYME A(Non-covalent)

COA.2: 22 residues within 4Å: Chain A: R.21, Y.23, Q.24, F.25, W.26, N.85, Y.86, V.87, L.154, C.155, V.156, R.161, S.162, R.164, A.166, P.167, I.170, G.190, V.191, L.193 Ligands: ALA-ASN-CYS-PHE-SER-LYS-PRO-ARG.1, MYR.6 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:Y.86, A:V.87, A:L.154, A:V.156, A:A.166 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 Water bridges: A:K.163 Salt bridges: A:R.21

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 4 residues within 4Å: Chain A: M.362, E.363, T.366, E.395 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.395 Water bridges: A:M.362, A:K.365, A:K.396 GOL.4: 8 residues within 4Å: Chain A: E.150, M.272, W.280, F.328, Y.329, V.400, L.401, Q.402 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.150, A:Y.329, A:Q.402 GOL.5: 11 residues within 4Å: Chain A: P.32, K.195, P.196, V.197, Y.383, L.384, W.387, K.388, C.389, P.390, S.391 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:V.197, A:L.384, A:L.384, A:C.389, A:C.389, A:S.391 Water bridges: A:K.195

1 x MYR: MYRISTIC ACID(Non-covalent)

MYR.6: 19 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: ALA-ASN-CYS-PHE-SER-LYS-PRO-ARG.1, COA.2 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:I.151, A:I.151, A:L.154, 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:F.153, 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
B

Glycylpeptide N-tetradecanoyltransferase 1

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