SMTL ID : 6pau.1

Structure of Human NMT2 with myristoyl-lysine peptide and CoA products

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.93 Å

Oligo State

monomer

Ligands

1 x LYS- VAL- LEU- SER- LYS- ILE- PHE: Arf6 peptide(Non-covalent)

LYS-VAL-LEU-SER-LYS-ILE-PHE.1: 37 residues within 4Å: Chain A: Y.67, V.68, E.69, D.70, D.71, D.72, M.74, F.75, R.76, F.77, N.133, F.134, L.135, T.169, A.170, G.171, Y.183, H.185, S.187, L.193, K.197, F.198, S.199, H.200, S.292, Y.307, V.336, G.355, I.356, G.357, D.358, G.359, N.360, L.361 Ligands: GOL.4, 4PS.12, MYR.14 26 PLIP interactions: 26 interactions with chain A Hydrophobic interactions: A:F.75, A:F.75, A:F.77, A:F.77, A:H.185, A:F.198, A:F.198 Hydrogen bonds: A:D.70, A:D.72, A:D.72, A:T.169, A:H.185, A:F.198, A:I.356, A:D.358, A:D.358, A:G.359 Water bridges: A:Y.67, A:Y.67, A:E.69, A:D.71, A:T.169, A:G.171, A:Y.307, A:Y.307 Salt bridges: A:H.200

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 9 residues within 4Å: Chain A: V.137, L.141, R.142, S.143, K.144, R.145, V.146, A.147 Ligands: 4PS.12 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:L.141

9 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 8 residues within 4Å: Chain A: N.66, Y.67, V.68, E.69, N.73, K.139, R.142 Ligands: 4PS.12 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.69, A:E.69, A:R.142, A:R.142 Water bridges: A:N.73 GOL.4: 12 residues within 4Å: Chain A: F.77, Y.79, Y.183, Y.288, L.290, Y.307, L.340, L.361, L.382, Q.383 Ligands: LYS-VAL-LEU-SER-LYS-ILE-PHE.1, LYS-VAL-LEU-SER-LYS-ILE-PHE.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.288, A:L.382, A:Q.383 Water bridges: A:T.169 GOL.5: 8 residues within 4Å: Chain A: K.176, P.177, I.178, Y.364, L.365, W.368, R.369, C.370 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.176, A:I.178, A:L.365, A:C.370 GOL.6: 5 residues within 4Å: Chain A: W.93, L.94, L.95, Q.96 Ligands: GOL.9 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.95, A:Q.96 GOL.7: 11 residues within 4Å: Chain A: I.116, E.131, P.251, M.253, W.261, F.309, Y.310, L.380, V.381, L.382, Q.383 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.310, A:Q.383, A:Q.383 GOL.8: 6 residues within 4Å: Chain A: Y.60, N.64, D.78, T.293, K.301, S.302 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.60, A:N.64, A:T.293 Water bridges: A:N.64, A:N.64 GOL.9: 5 residues within 4Å: Chain A: D.49, S.51, R.89, W.93 Ligands: GOL.6 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.49 GOL.10: 9 residues within 4Å: Chain A: P.91, G.92, P.117, A.118, N.119, K.128, D.254, E.257 Ligands: GOL.11 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:P.117, A:N.119, A:N.119, A:D.254 GOL.11: 8 residues within 4Å: Chain A: G.92, L.94, W.97, P.117, K.128, E.161, I.163 Ligands: GOL.10 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.92, A:K.128

1 x 4PS: 4'-diphospho pantetheine(Non-covalent)

4PS.12: 19 residues within 4Å: Chain A: N.66, Y.67, V.68, L.135, C.136, V.137, R.142, S.143, K.144, R.145, V.146, A.147, P.148, A.170, V.172 Ligands: LYS-VAL-LEU-SER-LYS-ILE-PHE.1, MG.2, GOL.3, MYR.14 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:Y.67, A:L.135, A:A.147 Hydrogen bonds: A:L.135, A:V.137, A:R.142, A:R.142, A:S.143, A:R.145, A:V.146, A:A.147 Salt bridges: A:R.145

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.13: 2 residues within 4Å: Chain A: R.209, K.212 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.209 Salt bridges: A:R.209, A:K.212

1 x MYR: MYRISTIC ACID(Non-covalent)

MYR.14: 18 residues within 4Å: Chain A: V.130, I.132, N.133, F.134, L.135, I.151, I.154, T.155, V.158, N.159, I.163, F.164, A.166, Y.168, T.169, Y.366 Ligands: LYS-VAL-LEU-SER-LYS-ILE-PHE.1, 4PS.12 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:V.130, A:I.132, A:I.132, A:I.132, A:L.135, A:I.151, A:I.154, A:T.155, A:V.158, A:Y.168, A:Y.168, A:Y.168, A:Y.366, A:Y.366 Hydrogen bonds: A:L.135

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kosciuk, T. et al., NMT1 and NMT2 are lysine myristoyltransferases regulating the ARF6 GTPase cycle. Nat Commun (2020)

Release Date

2020-03-11

Peptides

Glycylpeptide N-tetradecanoyltransferase 2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Glycylpeptide N-tetradecanoyltransferase 2