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

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

monomer

Ligands

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 10 residues within 4Å: Chain A: E.139, P.259, M.261, W.269, F.317, Y.318, L.388, V.389, L.390, Q.391 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.139, A:Y.318, A:Q.391, A:Q.391 GOL.2: 11 residues within 4Å: Chain A: P.21, K.184, P.185, V.186, Y.372, L.373, W.376, K.377, C.378, P.379, S.380 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:P.185, A:L.373, A:L.373, A:W.376, A:C.378 Water bridges: A:K.184

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

MYA.3: 36 residues within 4Å: Chain A: R.10, Y.12, Q.13, F.14, W.15, N.74, Y.75, V.76, I.140, N.141, F.142, L.143, C.144, V.145, R.150, S.151, K.152, R.153, V.154, A.155, P.156, I.159, T.163, V.166, H.167, I.171, F.172, Q.173, A.174, Y.176, T.177, L.182, Y.374 Ligands: GLY.4, MYR.12, COA.13 29 PLIP interactions: 29 interactions with chain A Hydrophobic interactions: A:Y.75, A:I.140, A:I.140, A:L.143, A:L.143, A:L.143, A:V.145, A:I.159, A:I.159, A:V.166, A:A.174, A:Y.176, A:Y.176, A:Y.374 Hydrogen bonds: A:R.10, A:Q.13, A:F.14, A:W.15, A:F.142, A:L.143, A:V.145, A:R.150, A:R.150, A:S.151, A:R.153, A:V.154, A:A.155 Water bridges: A:K.152, A:K.152

1 x GLY: GLYCINE(Non-covalent)

GLY.4: 8 residues within 4Å: Chain A: Y.75, N.141, T.177, A.178 Ligands: MYA.3, SER.5, MYR.12, COA.13 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.177 Water bridges: A:T.177

2 x SER: SERINE(Non-covalent)

SER.5: 5 residues within 4Å: Chain A: V.76, Y.191, Q.391 Ligands: GLY.4, ASN.6 7 PLIP interactions: 6 interactions with chain A, 1 Ligand-Ligand interactions Hydrogen bonds: A:Y.75, A:Y.75, A:Y.191, A:Q.391 Water bridges: A:N.141, A:Q.391, S.5 SER.8: 9 residues within 4Å: Chain A: Y.191, H.193, F.206, G.365, D.366, G.367 Ligands: ASN.6, LYS.7, LYS.9 5 PLIP interactions: 3 Ligand-Ligand interactions, 2 interactions with chain A Hydrogen bonds: K.7, A:D.366, A:G.367 Water bridges: K.7, K.7

1 x ASN: ASPARAGINE(Non-covalent)

ASN.6: 9 residues within 4Å: Chain A: V.76, F.85, G.179, Y.191, G.367, N.368 Ligands: SER.5, LYS.7, SER.8 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Ligand interactions Hydrogen bonds: A:Y.191, A:N.368, K.7 Water bridges: A:G.179, A:G.179, S.8

3 x LYS: LYSINE(Non-covalent)

LYS.7: 6 residues within 4Å: Chain A: V.76, F.83, F.85, Y.315 Ligands: ASN.6, SER.8 7 PLIP interactions: 2 Ligand-Ligand interactions, 5 interactions with chain A Hydrogen bonds: N.6, S.8, A:Y.315 Hydrophobic interactions: A:V.76, A:F.85 Water bridges: A:Y.315, A:N.346 LYS.9: 8 residues within 4Å: Chain A: D.80, H.193, F.206, G.365, D.366 Ligands: SER.8, PRO.10, LYS.11 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:F.206 Hydrogen bonds: A:D.366, A:D.366, A:D.366, K.9 LYS.11: 6 residues within 4Å: Chain A: R.190, H.208, I.364, G.365 Ligands: LYS.9, PRO.10 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Ligand interactions Hydrogen bonds: A:R.190, A:R.190, A:I.364 Salt bridges: A:H.208 Water bridges: K.11

1 x PRO: PROLINE(Non-covalent)

PRO.10: 6 residues within 4Å: Chain A: H.193, F.206, S.207, I.364 Ligands: LYS.9, LYS.11 2 PLIP interactions: 2 interactions with chain A, Hydrophobic interactions: A:H.193, A:F.206

1 x MYR: MYRISTIC ACID(Non-covalent)

MYR.12: 20 residues within 4Å: Chain A: W.15, Y.75, I.140, F.142, L.143, I.159, I.162, T.163, V.166, H.167, I.171, F.172, Q.173, A.174, Y.176, T.177, Y.374 Ligands: MYA.3, GLY.4, COA.13 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:I.140, A:I.140, A:I.140, A:L.143, A:L.143, A:I.159, A:I.159, A:I.162, A:V.166, A:A.174, A:Y.176, A:Y.176, A:Y.176, A:Y.374 Hydrogen bonds: A:F.142, A:L.143

1 x COA: COENZYME A(Non-covalent)

COA.13: 24 residues within 4Å: Chain A: R.10, Y.12, Q.13, F.14, W.15, N.74, Y.75, V.76, L.143, C.144, V.145, R.150, S.151, K.152, R.153, V.154, A.155, P.156, I.159, T.177, L.182 Ligands: MYA.3, GLY.4, MYR.12 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:Y.75, A:L.143, A:V.145 Hydrogen bonds: A:R.10, A:Q.13, A:F.14, A:W.15, A:V.145, A:R.150, A:S.151, A:R.153, A:V.154, A:A.155 Water bridges: A:K.152, A:K.152

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

2019-03-27

Peptides

Glycylpeptide N-tetradecanoyltransferase 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Glycylpeptide N-tetradecanoyltransferase 1

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