SMTL ID : 6sk8.1 (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 ASP- CYS- PHE- SER- LYS- PRO- ARG: Apoptosis-inducing factor 3(Non-covalent)

ASP-CYS-PHE-SER-LYS-PRO-ARG.1: 20 residues within 4Å: Chain A: V.87, E.88, D.89, M.93, F.94, F.96, G.190, Y.202, H.204, K.216, F.217, S.218, Y.307, S.311, Y.326, I.375, G.376, D.377, G.378, N.379 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:D.89, A:F.94, A:F.96, A:H.204, A:F.217 Hydrogen bonds: A:Y.202, A:Y.202, A:Y.202, A:I.375, A:D.377, A:D.377, A:G.378, A:G.378 Water bridges: A:Y.98, A:N.152, A:N.152, A:N.152, A:G.190, A:Y.307, A:Y.307, A:Y.307

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

MYA.2: 32 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, F.183, Q.184, A.185, Y.187, T.188, L.193, Y.385 31 PLIP interactions: 31 interactions with chain A Hydrophobic interactions: A:Y.86, A:I.151, A:L.154, A:L.154, A:V.156, A:A.166, A:I.170, A:V.177, A:A.185, A:Y.187, 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:K.163, A:K.163 Salt bridges: A:R.21

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 4 residues within 4Å: Chain A: K.211, H.319, K.320, S.321 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.211, A:K.320, A:S.321, A:S.321 Water bridges: A:D.354 GOL.4: 5 residues within 4Å: Chain A: H.332, T.333, Q.334, T.335, P.336 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.332, A:Q.334 GOL.5: 9 residues within 4Å: Chain A: P.32, K.195, P.196, V.197, Y.383, L.384, W.387, K.388, C.389 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:L.384, A:L.384, A:W.387, A:C.389 Water bridges: A:K.195, A:P.196, A:S.391

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.6: 5 residues within 4Å: Chain A: L.67, L.69, R.108, W.112, H.117 Ligand excluded by PLIP

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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