SMTL ID : 6sk2.1 (1 other biounit)

HsNMT1 in complex with both MyrCoA and Acetylated-GKSFSKPR peptide reveals N-terminal Lysine Myristoylation

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

monomer

Ligands

1 x ACE- GLY- LYS- SER- PHE- SER- LYS- PRO- ARG: Apoptosis-inducing factor 3(Non-covalent)

ACE-GLY-LYS-SER-PHE-SER-LYS-PRO-ARG.1: 30 residues within 4Å: Chain A: Y.86, V.87, E.88, D.89, D.91, F.94, F.96, Y.98, N.152, T.188, A.189, G.190, Y.202, H.204, F.217, H.219, Y.307, L.309, S.311, Y.326, I.375, G.376, D.377, G.378, N.379, L.380, L.401, Q.402 Ligands: COA.4, MYR.5 25 PLIP interactions: 25 interactions with chain A Hydrophobic interactions: A:D.89, A:F.94, A:F.94, A:F.96 Hydrogen bonds: A:D.89, A:D.89, A:D.91, A:Y.98, A:T.188, A:G.190, A:Y.202, A:Y.202, A:Y.307, A:I.375, A:D.377, A:D.377, A:D.377, A:G.378, A:N.379 Water bridges: A:E.88, A:N.152, A:N.152, A:T.188, A:I.375 Salt bridges: A:H.219

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 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:P.196, A:L.384, A:L.384, A:C.389, A:C.389 Water bridges: A:K.195, A:S.391 GOL.3: 5 residues within 4Å: Chain A: K.211, T.318, H.319, K.320, S.321 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.211, A:H.319, A:K.320, A:S.321

1 x COA: COENZYME A(Non-covalent)

COA.4: 25 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, K.163, R.164, V.165, A.166, P.167, I.170, A.189, G.190, V.191, L.193 Ligands: ACE-GLY-LYS-SER-PHE-SER-LYS-PRO-ARG.1, MYR.5 16 PLIP interactions: 16 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:K.163, A:R.164, A:V.165, A:A.166 Salt bridges: A:R.21

1 x MYR: MYRISTIC ACID(Non-covalent)

MYR.5: 18 residues within 4Å: Chain A: W.26, 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-GLY-LYS-SER-PHE-SER-LYS-PRO-ARG.1, COA.4 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:I.151, A:I.170, A:V.177, A:A.185, A:Y.187, 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

Dian, C. et al., High-resolution snapshots of human N-myristoyltransferase in action illuminate a mechanism promoting N-terminal Lys and Gly myristoylation. Nat Commun (2020)

Release Date

2020-03-18

Peptides

Glycylpeptide N-tetradecanoyltransferase 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Glycylpeptide N-tetradecanoyltransferase 1

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