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

HsNMT1 in complex with both MyrCoA and Acetylated-GNCFSKPR substrates

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

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

ACE-GLY-ASN-CYS-PHE-SER-LYS-PRO.1: 29 residues within 4Å: Chain A: Y.86, V.87, E.88, D.89, D.90, D.91, F.94, R.95, F.96, Y.98, N.152, T.188, A.189, G.190, Y.202, H.204, F.217, Y.307, L.309, S.311, Y.326, I.375, G.376, D.377, N.379, L.380, L.401, Q.402 Ligands: MYA.2 25 PLIP interactions: 25 interactions with chain A Hydrophobic interactions: A:D.89, A:F.94, A:F.94, A:F.96, A:F.96, A:H.204, A:F.217, A:F.217, A:Y.307, A:L.309, A:Y.326 Hydrogen bonds: A:D.89, A:D.90, A:D.91, A:T.188, A:T.188, A:G.190, A:Y.202, A:Y.307, A:Y.307, A:D.377, A:D.377, A:Q.402 Water bridges: A:N.152, A:T.188

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, 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 Ligands: ACE-GLY-ASN-CYS-PHE-SER-LYS-PRO.1 37 PLIP interactions: 37 interactions with chain A Hydrophobic interactions: A:Y.86, A:V.87, A:I.151, 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: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:R.21, A:K.163, A:K.163, A:R.164, A:R.164 Salt bridges: A:R.21, A:R.164, A:R.164

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

CL.3: 4 residues within 4Å: Chain A: V.38, K.195, P.390, S.391 Ligand excluded by PLIP

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 10 residues within 4Å: Chain A: E.150, P.270, M.272, W.280, F.328, Y.329, L.399, V.400, L.401, Q.402 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.150, A:Y.329, A:Q.402, 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:K.195, A:K.195, A:L.384, A:L.384, A:C.389, 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
A

Glycylpeptide N-tetradecanoyltransferase 1

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