SMTL ID : 5o9v.1 (1 other biounit)

HsNMT1 in complex with CoA and Myristoylated-GGCFSKPK octapeptide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

monomer

Ligands

1 x GLY- GLY- CYS- PHE- SER- LYS- PRO- LYS: Apoptosis-inducing factor 3(Non-covalent)

GLY-GLY-CYS-PHE-SER-LYS-PRO-LYS.1: 25 residues within 4Å: Chain A: Y.86, V.87, E.88, D.89, D.91, F.94, F.96, N.152, T.188, A.189, G.190, Y.202, H.204, F.217, S.218, S.311, I.375, G.376, D.377, G.378, N.379, L.380 Ligands: COA.2, GOL.3, MYR.7 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:D.89, A:F.94, A:F.96, A:F.217, A:F.217 Hydrogen bonds: A:Y.86, A:Y.86, A:D.90, A:T.188, A:T.188, A:I.375, A:D.377, A:D.377, A:D.377, A:D.377, A:G.378, A:G.378 Water bridges: A:T.188, A:T.188, A:Y.326, A:Y.326, A:I.375

1 x COA: COENZYME A(Non-covalent)

COA.2: 25 residues within 4Å: Chain A: R.21, Y.23, Q.24, F.25, W.26, N.85, Y.86, V.87, L.154, C.155, V.156, R.161, S.162, K.163, R.164, V.165, A.166, P.167, I.170, T.188, A.189, L.193 Ligands: GLY-GLY-CYS-PHE-SER-LYS-PRO-LYS.1, GLY-GLY-CYS-PHE-SER-LYS-PRO-LYS.1, MYR.7 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:Y.86, A:V.87, A:L.154, A:V.156, A:A.166 Hydrogen bonds: A:Q.24, A:F.25, A:W.26, A:L.154, A:V.156, A:R.161, A:S.162, A:R.164, A:V.165, A:A.166 Water bridges: A:R.21, A:R.161, A:K.163, A:K.163 Salt bridges: A:R.21, A:R.164, A:R.164

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 11 residues within 4Å: Chain A: F.96, Y.98, Y.202, Y.307, L.309, Y.326, L.380, L.401, Q.402 Ligands: GLY-GLY-CYS-PHE-SER-LYS-PRO-LYS.1, GLY-GLY-CYS-PHE-SER-LYS-PRO-LYS.1 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Y.202, A:Y.307, A:Y.307, A:Q.402 Water bridges: A:Y.98, A:N.152 GOL.4: 10 residues within 4Å: Chain A: P.32, K.195, P.196, V.197, Y.383, L.384, W.387, K.388, C.389, S.391 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:L.384, A:L.384, A:W.387, A:C.389 Water bridges: A:K.195, A:P.196, A:S.391 GOL.5: 5 residues within 4Å: Chain A: K.211, T.318, H.319, K.320, S.321 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.211, A:K.211, A:H.319, A:K.320, A:S.321

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.6: 6 residues within 4Å: Chain A: L.67, D.68, L.69, R.108, W.112, H.117 Ligand excluded by PLIP

1 x MYR: MYRISTIC ACID(Non-covalent)

MYR.7: 17 residues within 4Å: Chain A: W.26, I.151, N.152, F.153, L.154, I.170, T.174, V.177, H.178, I.182, F.183, A.185, Y.187, T.188, Y.385 Ligands: GLY-GLY-CYS-PHE-SER-LYS-PRO-LYS.1, COA.2 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:I.151, A:I.151, A:I.151, A:L.154, A:I.170, A:I.170, A:T.174, A:V.177, A:A.185, A:Y.187, A:Y.187, A:Y.187, A:Y.385 Hydrogen bonds: A:L.154

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Castrec, B. et al., Structural and genomic decoding of human and plant myristoylomes reveals a definitive recognition pattern. Nat. Chem. Biol. (2018)

Release Date

2018-06-27

Peptides

Glycylpeptide N-tetradecanoyltransferase 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Glycylpeptide N-tetradecanoyltransferase 1

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