SMTL ID : 7rk3.1

Crystal structure of human N-myristoyltransferase 1 fragment (residues 109-496) bound to diacylated human Arf6 octapeptide and Coenzyme A

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

monomer

Ligands

1 x GLY- LYS- VAL- LEU- SER- LYS- ILE- PHE: ADP-ribosylation factor 6(Non-covalent)

GLY-LYS-VAL-LEU-SER-LYS-ILE-PHE.1: 30 residues within 4Å: Chain A: Y.75, V.76, E.77, D.78, D.80, M.82, F.83, R.84, F.85, Y.87, N.141, T.177, G.179, Y.191, H.193, S.195, F.206, S.207, H.208, S.300, I.364, G.365, D.366, G.367, N.368, L.369, Q.391 Ligands: 4PS.2, MYR.3, 6NA.4 26 PLIP interactions: 26 interactions with chain A Hydrophobic interactions: A:F.83, A:Y.191, A:H.193, A:F.206, A:F.206 Hydrogen bonds: A:D.80, A:Y.191, A:Y.191, A:Y.191, A:F.206, A:I.364, A:D.366, A:D.366, A:D.366, A:D.366, A:G.367 Water bridges: A:Y.75, A:Y.75, A:E.77, A:D.79, A:D.79, A:T.177, A:T.177, A:T.177, A:Y.315 Salt bridges: A:H.208

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

4PS.2: 16 residues within 4Å: Chain A: 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, A.178 Ligands: GLY-LYS-VAL-LEU-SER-LYS-ILE-PHE.1, MYR.3 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:Y.75, A:V.76, A:L.143, A:A.155 Hydrogen bonds: A:L.143, A:V.145, A:S.151, A:R.153, A:V.154, A:A.155 Water bridges: A:K.152, A:K.152 Salt bridges: A:R.153

1 x MYR: MYRISTIC ACID(Non-covalent)

MYR.3: 16 residues within 4Å: Chain A: I.140, N.141, F.142, L.143, I.159, T.163, V.166, I.171, F.172, Q.173, A.174, Y.176, T.177, Y.374 Ligands: GLY-LYS-VAL-LEU-SER-LYS-ILE-PHE.1, 4PS.2 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:I.140, A:L.143, A:I.159, A:V.166, A:A.174, A:Y.176, A:Y.176, A:Y.374 Hydrogen bonds: A:L.143

1 x 6NA: HEXANOIC ACID(Non-covalent)

6NA.4: 12 residues within 4Å: Chain A: Y.191, Y.296, Y.315, S.316, N.346, A.347, L.348, V.389, L.390, Q.391 Ligands: GLY-LYS-VAL-LEU-SER-LYS-ILE-PHE.1, GLY-LYS-VAL-LEU-SER-LYS-ILE-PHE.1 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:Y.191, A:Y.315, A:L.348, A:V.389 Hydrogen bonds: A:Y.296 Water bridges: A:T.177

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fenwick, M.K. et al., Crystal structure of human N-myristoyltransferase 1 fragment (residues 109-496) bound to diacylated human Arf6 octapeptide and Coenzyme A. To Be Published

Release Date

2022-07-27

Peptides

Glycylpeptide N-tetradecanoyltransferase 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Glycylpeptide N-tetradecanoyltransferase 1

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