SMTL ID : 6pav.1

Structure of Human NMT1 with products CoA and myristoyl-lysine peptide with acetylated N-terminus

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.52 Å

Oligo State

homo-dimer

Ligands

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

ACE-LYS-VAL-LEU-SER-LYS-ILE-PHE.1: 39 residues within 4Å: Chain A: Y.72, V.73, E.74, D.75, D.76, D.77, M.79, F.80, R.81, F.82, Y.84, N.138, F.139, L.140, T.174, A.175, G.176, R.187, Y.188, H.190, K.202, F.203, S.204, H.205, Y.293, L.295, S.297, L.308, Y.312, G.360, I.361, G.362, D.363, G.364, N.365, L.366, Q.388 Ligands: COA.3, MYR.6 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Ligand interactions Hydrogen bonds: A:Y.188, V.0

1 x GLY- LYS- VAL- LEU- SER- LYS- ILE- PHE: ARF6 peptide(Non-covalent)

GLY-LYS-VAL-LEU-SER-LYS-ILE-PHE.2: 38 residues within 4Å: Chain B: Y.72, V.73, E.74, D.75, D.76, D.77, M.79, F.80, R.81, F.82, Y.84, N.138, F.139, L.140, T.174, A.175, G.176, R.187, Y.188, H.190, S.192, K.202, F.203, S.204, H.205, Y.293, S.297, Y.312, G.360, I.361, G.362, D.363, G.364, N.365, L.366, Q.388 Ligands: COA.7, MYR.10 20 PLIP interactions: 20 interactions with chain B Hydrophobic interactions: B:F.80, B:F.82, B:F.82, B:F.82, B:H.190, B:F.203, B:F.203, B:I.361, B:D.363, B:L.366 Hydrogen bonds: B:D.75, B:D.76, B:Y.84, B:Y.188, B:F.203, B:I.361, B:D.363, B:D.363, B:D.363, B:G.364

2 x COA: COENZYME A(Non-covalent)

COA.3: 22 residues within 4Å: Chain A: Y.9, Q.10, F.11, W.12, N.71, Y.72, V.73, L.140, C.141, V.142, R.147, S.148, K.149, R.150, V.151, A.152, P.153, I.156, A.175, L.179 Ligands: ACE-LYS-VAL-LEU-SER-LYS-ILE-PHE.1, MYR.6 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:Y.72, A:V.73, A:V.142 Hydrogen bonds: A:F.11, A:W.12, A:W.12, A:V.142, A:R.147, A:R.147, A:S.148, A:R.150, A:V.151, A:A.152 COA.7: 25 residues within 4Å: Chain B: S.8, Y.9, Q.10, F.11, W.12, N.71, Y.72, V.73, L.140, C.141, V.142, R.147, S.148, K.149, R.150, V.151, A.152, P.153, I.156, A.175, G.176, V.177, L.179 Ligands: GLY-LYS-VAL-LEU-SER-LYS-ILE-PHE.2, MYR.10 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:Y.72, B:V.73, B:V.142, B:A.152 Hydrogen bonds: B:Q.10, B:F.11, B:W.12, B:L.140, B:V.142, B:R.147, B:S.148, B:R.150, B:V.151, B:A.152

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 11 residues within 4Å: Chain A: P.18, K.181, P.182, V.183, Y.369, L.370, W.373, K.374, C.375, P.376, S.377 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:K.181, A:V.183, A:L.370, A:L.370, A:C.375, A:C.375 GOL.5: 11 residues within 4Å: Chain A: A.123, E.136, P.256, M.258, W.266, F.314, Y.315, L.385, V.386, L.387, Q.388 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.136, A:Y.315, A:Q.388 GOL.8: 11 residues within 4Å: Chain B: P.18, V.24, K.181, P.182, V.183, Y.369, L.370, W.373, K.374, C.375, S.377 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:L.370, B:L.370, B:W.373, B:C.375, B:C.375 GOL.9: 11 residues within 4Å: Chain B: A.123, E.136, P.256, M.258, W.266, F.314, Y.315, L.385, V.386, L.387, Q.388 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:E.136, B:Y.315, B:V.386, B:Q.388, B:Q.388 Water bridges: B:W.266

2 x MYR: MYRISTIC ACID(Non-covalent)

MYR.6: 23 residues within 4Å: Chain A: W.12, Y.72, I.118, V.135, I.137, N.138, F.139, L.140, I.156, I.159, T.160, V.163, H.164, I.168, F.169, Q.170, A.171, Y.173, T.174, A.175, Y.371 Ligands: ACE-LYS-VAL-LEU-SER-LYS-ILE-PHE.1, COA.3 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:V.135, A:I.137, A:I.137, A:I.137, A:I.156, A:T.160, A:V.163, A:A.171, A:Y.173, A:Y.173, A:Y.173, A:Y.371 Hydrogen bonds: A:L.140 MYR.10: 21 residues within 4Å: Chain B: W.12, Y.72, I.118, V.135, I.137, N.138, F.139, L.140, I.156, I.159, T.160, V.163, H.164, I.168, F.169, Q.170, A.171, Y.173, Y.371 Ligands: GLY-LYS-VAL-LEU-SER-LYS-ILE-PHE.2, COA.7 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:W.12, B:I.137, B:I.137, B:I.137, B:L.140, B:I.156, B:I.159, B:V.163, B:A.171, B:Y.173, B:Y.173, B:Y.173, B:Y.371 Hydrogen bonds: B:Y.72, B:L.140

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 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

Glycylpeptide N-tetradecanoyltransferase 1