SMTL ID : 6sk8.2 (1 other biounit)

DeltaC3 C-terminal truncation of HsNMT1 in complex with MyrCoA and GDCFSKPR substrates

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.87 Å

Oligo State

monomer

Ligands

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

GLY-ASP-CYS-PHE-SER-LYS-PRO-ARG.1: 25 residues within 4Å: Chain A: V.87, E.88, D.89, M.93, F.94, F.96, Y.98, N.152, T.188, G.190, R.201, Y.202, H.204, F.217, S.218, H.219, Y.307, S.311, Y.326, I.375, G.376, D.377, G.378, N.379, L.380 24 PLIP interactions: 24 interactions with chain A Hydrophobic interactions: A:D.89, A:F.94, A:F.94, A:F.96, A:F.96 Hydrogen bonds: A:D.89, A:Y.98, A:Y.98, A:T.188, 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:G.378 Water bridges: A:N.152, A:T.188, A:T.188, A:T.188, A:G.190 Salt bridges: A:H.219

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

MYA.2: 34 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, L.160, 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 27 PLIP interactions: 27 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:I.170, A:V.177, A:A.185, A:Y.187, A:Y.385 Hydrogen bonds: A:Q.24, A:F.25, A:W.26, A:F.153, A:L.154, A:L.154, A:V.156, A:R.161, A:R.161, A:S.162, A:K.163, A:R.164, A:V.165, A:A.166 Salt bridges: A:R.21

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 5 residues within 4Å: Chain A: N.138, V.271, M.272, S.273, E.276 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.138, A:V.271, A:M.272, A:S.273 GOL.4: 4 residues within 4Å: Chain A: K.147, E.180, G.181, I.182 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.147, A:K.147 Water bridges: A:G.181 GOL.5: 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 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:P.196, A:V.197, A:L.384, A:L.384, A:W.387, A:C.389 Water bridges: A:K.195

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
B

Glycylpeptide N-tetradecanoyltransferase 1

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