SMTL ID : 4c2z.1 (1 other biounit)

Human N-myristoyltransferase (NMT1) with Myristoyl-CoA and inhibitor bound

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.08 Å

Oligo State

monomer

Ligands

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

MYA.1: 35 residues within 4Å: Chain A: Y.31, Q.32, F.33, W.34, N.93, Y.94, V.95, I.159, N.160, F.161, L.162, C.163, V.164, R.169, S.170, K.171, R.172, V.173, A.174, P.175, I.178, T.182, V.185, H.186, I.190, F.191, Q.192, A.193, Y.195, T.196, A.197, L.201, Y.393 Ligands: 646.2, MG.3 29 PLIP interactions: 29 interactions with chain A Hydrophobic interactions: A:W.34, A:W.34, A:Y.94, A:I.159, A:L.162, A:V.164, A:I.178, A:V.185, A:A.193, A:Y.195, A:Y.195, A:Y.195, A:Y.393 Hydrogen bonds: A:Q.32, A:F.33, A:W.34, A:L.162, A:L.162, A:V.164, A:R.169, A:S.170, A:R.172, A:V.173, A:A.174 Water bridges: A:R.172, A:R.172, A:G.198 Salt bridges: A:R.172, A:R.172

1 x 646: 2,6-dichloro-4-(2-piperazin-1-ylpyridin-4-yl)-N-(1,3,5-trimethyl-1H-pyrazol-4-yl)benzenesulfonamide(Non-covalent)

646.2: 19 residues within 4Å: Chain A: Y.94, V.95, E.96, D.97, F.102, F.104, N.160, T.196, G.198, Y.210, H.212, F.225, S.319, L.330, Y.334, D.385, L.388, Q.410 Ligands: MYA.1 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:V.95, A:D.97, A:F.104, A:Y.210, A:F.225, A:L.330, A:L.388 Hydrogen bonds: A:T.196, A:G.198, A:S.319, A:N.365 Water bridges: A:Y.94 pi-Stacking: A:Y.210 Halogen bonds: A:Y.334

1 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 7 residues within 4Å: Chain A: L.168, R.169, S.170, K.171, R.172, V.173 Ligands: MYA.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:L.168

1 x CIT: CITRIC ACID(Non-functional Binders)

CIT.4: 6 residues within 4Å: Chain A: T.36, Q.37, P.38, E.53, K.56, R.179 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:T.36, A:Q.37 Water bridges: A:Q.37, A:K.56, A:R.179, A:R.179, A:Y.393 Salt bridges: A:K.56, A:R.179

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 11 residues within 4Å: Chain A: P.40, K.203, P.204, V.205, Y.391, L.392, W.395, K.396, C.397, P.398, S.399 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:P.204, A:L.392, A:L.392, A:W.395, A:C.397 Water bridges: A:K.203 GOL.6: 10 residues within 4Å: Chain A: I.143, E.158, M.280, W.288, F.336, Y.337, L.407, V.408, L.409, Q.410 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.158, A:W.288, A:Y.337, A:Q.410

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

CL.7: 4 residues within 4Å: Chain A: S.214, P.217, S.226, Y.241 Ligand excluded by PLIP CL.8: 4 residues within 4Å: Chain A: Q.32, F.33, R.172, P.175 Ligand excluded by PLIP CL.9: 3 residues within 4Å: Chain A: V.46, P.398, S.399 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Thinon, E. et al., Chemical Proteomics Defines the Mammalian N- Myristoylated Proteome in Live Cells Global Profiling of Co- and Post-Translationally N-Myristoylated Proteomes in Human Cells. Nat.Commun. (2014)

Release Date

2014-10-01

Peptides

GLYCYLPEPTIDE N-TETRADECANOYLTRANSFERASE 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

GLYCYLPEPTIDE N-TETRADECANOYLTRANSFERASE 1

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