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

DeltaC2 C-terminal truncation of HsNMT1 in complex with MyrCoA and GNCFSKPR substrates

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

monomer

Ligands

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

GLY-ASN-CYS-PHE-SER-LYS-PRO-ARG.1: 31 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, L.309, S.311, Y.326, I.375, G.376, D.377, G.378, N.379, L.380 Ligands: COA.4, MYR.6, MYA.7 23 PLIP interactions: 23 interactions with chain A Hydrophobic interactions: A:D.89, A:F.94, A:F.94, A:F.96, A:H.204, A:F.217, A:F.217, A:I.375 Hydrogen bonds: A:Y.86, A:D.89, A:D.90, A:D.91, A:D.91, A:Y.202, A:I.375, A:G.376, A:D.377, A:D.377, A:G.378, A:G.378 Water bridges: A:Y.98, A:T.188 Salt bridges: A:H.219

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 9 residues within 4Å: Chain A: P.32, K.195, P.196, V.197, Y.383, L.384, W.387, K.388, C.389 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:P.196, A:L.384, A:W.387, A:C.389 GOL.3: 5 residues within 4Å: Chain A: Q.29, E.45, K.48, Y.56, R.171 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.45, A:K.48, A:R.171

1 x COA: COENZYME A(Non-covalent)

COA.4: 23 residues within 4Å: Chain A: 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, T.188, A.189, L.193 Ligands: GLY-ASN-CYS-PHE-SER-LYS-PRO-ARG.1, MYR.6, MYA.7 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:Y.86, A:V.87, A:L.154, A:L.154, A:V.156 Hydrogen bonds: A:Q.24, A:F.25, A:W.26, A:L.154, A:V.156, A:R.161, A:S.162, A:K.163, A:R.164, A:V.165, A:A.166 Water bridges: A:S.162

1 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 2 residues within 4Å: Chain A: H.332, T.335 No protein-ligand interaction detected (PLIP)

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, F.183, Q.184, A.185, Y.187, T.188, Y.385 Ligands: GLY-ASN-CYS-PHE-SER-LYS-PRO-ARG.1, COA.4, MYA.7 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:W.26, A:I.151, A:I.151, A:L.154, A:I.170, A:T.174, A:V.177, A:A.185, A:Y.187, A:Y.187, A:Y.187, A:Y.187, A:Y.385 Hydrogen bonds: A:Y.86, A:F.153, A:L.154

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

MYA.7: 34 residues within 4Å: Chain A: 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 Ligands: GLY-ASN-CYS-PHE-SER-LYS-PRO-ARG.1, COA.4, MYR.6 31 PLIP interactions: 31 interactions with chain A Hydrophobic interactions: A:Y.86, A:V.87, A:I.151, A:I.151, A:I.151, A:L.154, A:L.154, A:L.154, A:V.156, A:I.170, A:I.170, A:T.174, A:V.177, A:A.185, A:Y.187, A:Y.187 Hydrogen bonds: 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:K.163, A:R.164, A:V.165, A:A.166

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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