SMTL ID : 4c7h.1

Leismania major N-myristoyltransferase in complex with a peptidomimetic (-NH2) molecule

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

monomer

Ligands

1 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 8 residues within 4Å: Chain A: L.165, R.166, E.167, K.168, R.169, L.170 Ligands: COA.3, MYA.4 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:L.165

1 x EN5: N-(10-AMINODECANOYL)-L-SERYL-N-(2-CYCLOHEXYLETHYL)-L-LYSINAMIDE(Non-covalent)

EN5.2: 25 residues within 4Å: Chain A: Y.70, D.73, D.74, D.75, M.77, F.78, N.157, T.193, G.195, Y.207, H.209, S.211, F.222, S.223, Y.243, G.383, A.384, G.385, D.386, G.387, L.389 Ligands: COA.3, MYA.4, ENF.5, DMS.7 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:F.78, A:Y.207, A:F.222, A:F.222 Hydrogen bonds: A:D.75, A:D.75, A:T.193, A:F.222, A:D.386, A:D.386, A:G.387 Water bridges: A:D.74, A:N.157, A:N.157, A:T.193, A:T.193

1 x COA: COENZYME A(Non-covalent)

COA.3: 23 residues within 4Å: Chain A: H.2, A.3, F.4, W.5, N.69, Y.70, V.71, L.159, C.160, V.161, R.166, E.167, K.168, R.169, L.170, A.171, P.172, T.193, L.198 Ligands: MG.1, EN5.2, MYA.4, ENF.5 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:Y.70, A:V.71, A:L.159, A:V.161 Hydrogen bonds: A:A.3, A:F.4, A:W.5, A:L.159, A:V.161, A:R.166, A:E.167, A:R.169, A:L.170, A:A.171 Water bridges: A:H.2, A:E.167, A:R.169, A:R.169, A:R.169 Salt bridges: A:H.2, A:R.169, A:R.169

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

MYA.4: 34 residues within 4Å: Chain A: H.2, A.3, F.4, W.5, N.69, Y.70, V.71, I.156, N.157, F.158, L.159, C.160, V.161, R.166, E.167, K.168, R.169, L.170, A.171, P.172, T.179, V.182, N.183, W.188, Q.189, A.190, Y.192, T.193, L.198, Y.394 Ligands: MG.1, EN5.2, COA.3, ENF.5 38 PLIP interactions: 38 interactions with chain A Hydrophobic interactions: A:W.5, A:Y.70, A:V.71, A:I.156, A:I.156, A:L.159, A:L.159, A:L.159, A:V.161, A:V.182, A:A.190, A:Y.192, A:Y.192, A:Y.394, A:Y.394 Hydrogen bonds: A:A.3, A:F.4, A:W.5, A:Y.70, A:F.158, A:L.159, A:L.159, A:V.161, A:R.166, A:R.166, A:E.167, A:R.169, A:L.170, A:A.171 Water bridges: A:H.2, A:H.2, A:E.167, A:R.169, A:R.169, A:R.169 Salt bridges: A:H.2, A:R.169, A:R.169

1 x ENF: N-{(5E)-10-[(9E)-TETRADEC-9-ENOYLAMINO]DEC-5-ENOYL}-L-SERYL-N-(2-CYCLOHEXYLETHYL)-L-LYSINAMIDE(Non-covalent)

ENF.5: 38 residues within 4Å: Chain A: W.5, Y.70, V.71, D.73, D.74, D.75, M.77, F.78, I.156, N.157, F.158, L.159, T.179, V.182, N.183, W.188, Q.189, A.190, Y.192, T.193, G.195, Y.207, H.209, S.211, F.222, S.223, Y.243, G.383, A.384, G.385, D.386, G.387, L.389, Y.394 Ligands: EN5.2, COA.3, MYA.4, DMS.7 26 PLIP interactions: 26 interactions with chain A Hydrophobic interactions: A:W.5, A:V.71, A:F.78, A:I.156, A:L.159, A:L.159, A:V.182, A:A.190, A:Y.192, A:Y.192, A:Y.207, A:F.222, A:F.222, A:Y.394 Hydrogen bonds: A:Y.70, A:Y.70, A:D.75, A:F.158, A:L.159, A:T.193, A:F.222, A:D.386, A:D.386, A:G.387 Water bridges: A:D.74, A:T.193

2 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.6: 8 residues within 4Å: Chain A: F.80, Y.82, Y.207, Y.316, I.318, Y.335, M.410, L.411 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Y.335 DMS.7: 5 residues within 4Å: Chain A: F.78, F.80, S.320 Ligands: EN5.2, ENF.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.320

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Olaleye, T.O. et al., Peptidomimetic Inhibitors of N-Myristoyltransferase from Human Malaria and Leishmaniasis Parasites. Org.Biomol.Chem. (2014)

Release Date

2014-09-24

Peptides

GLYCYLPEPTIDE N-TETRADECANOYLTRANSFERASE: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

GLYCYLPEPTIDE N-TETRADECANOYLTRANSFERASE

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