SMTL ID : 6ehj.2 (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: 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:C.378, A:C.378 Water bridges: A:K.184 GOL.2: 10 residues within 4Å: Chain A: A.126, E.139, P.259, M.261, W.269, Y.318, L.388, V.389, L.390, Q.391 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.139, A:Q.391, A:Q.391

1 x COA: COENZYME A(Non-covalent)

COA.3: 22 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, R.153, V.154, A.155, P.156, T.177, A.178, L.182 Ligands: MYR.4, GLY.5 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:Y.75, A:V.76, A:L.143, A:V.145 Hydrogen bonds: A:Q.13, A:F.14, A:W.15, A:L.143, A:V.145, A:R.150, A:S.151, A:R.153, A:V.154, A:A.155 Water bridges: A:K.152

1 x MYR: MYRISTIC ACID(Non-covalent)

MYR.4: 18 residues within 4Å: Chain A: W.15, I.140, N.141, F.142, L.143, I.159, T.163, V.166, H.167, I.171, F.172, Q.173, A.174, Y.176, T.177, Y.374 Ligands: COA.3, GLY.5 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:I.140, A:I.140, A:I.140, A:L.143, A:I.159, 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 GLY: GLYCINE(Non-covalent)

GLY.5: 7 residues within 4Å: Chain A: Y.75, N.141, T.177, A.178 Ligands: COA.3, MYR.4, SER.6 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.177 Water bridges: A:T.177, A:G.179

2 x SER: SERINE(Non-covalent)

SER.6: 7 residues within 4Å: Chain A: V.76, F.85, Y.87, Y.191, Q.391 Ligands: GLY.5, ASN.7 8 PLIP interactions: 7 interactions with chain A, 1 Ligand-Ligand interactions Hydrogen bonds: A:Y.75, A:Y.75, A:Y.87, A:Q.391 Water bridges: A:N.141, A:T.177, A:Y.191, S.6 SER.9: 9 residues within 4Å: Chain A: Y.191, H.193, F.206, G.365, D.366, G.367 Ligands: ASN.7, LYS.8, LYS.10 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Ligand interactions Hydrogen bonds: A:D.366, A:G.367, K.8 Water bridges: K.8, S.9

1 x ASN: ASPARAGINE(Non-covalent)

ASN.7: 10 residues within 4Å: Chain A: V.76, F.85, G.179, Y.191, G.367, N.368, L.369 Ligands: SER.6, LYS.8, SER.9 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Ligand interactions Hydrophobic interactions: A:Y.191 Hydrogen bonds: A:Y.191, A:N.368, K.8, S.9 Water bridges: A:G.179

3 x LYS: LYSINE(Non-covalent)

LYS.8: 9 residues within 4Å: Chain A: V.76, E.77, D.78, F.83, F.85, S.300, Y.315 Ligands: ASN.7, SER.9 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Ligand interactions Hydrophobic interactions: A:D.78, A:F.85 Hydrogen bonds: A:Y.315, A:Y.315, N.7, S.9 LYS.10: 10 residues within 4Å: Chain A: D.78, D.79, D.80, H.193, F.206, G.365, D.366 Ligands: SER.9, PRO.11, LYS.12 6 PLIP interactions: 6 interactions with chain A, Hydrophobic interactions: A:F.206 Hydrogen bonds: A:D.78, A:D.80, A:D.80, A:D.366, A:D.366 LYS.12: 4 residues within 4Å: Chain A: I.364, G.365 Ligands: LYS.10, PRO.11 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.364 Hydrogen bonds: A:I.364

1 x PRO: PROLINE(Non-covalent)

PRO.11: 5 residues within 4Å: Chain A: H.193, F.206, I.364 Ligands: LYS.10, LYS.12 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.206

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
B

Glycylpeptide N-tetradecanoyltransferase 1

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