SMTL ID : 5igw.1

Macrolide 2'-phosphotransferase type II - complex with GDP and clarithromycin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

monomer

Ligands

1 x GDP: GUANOSINE-5'-DIPHOSPHATE(Non-covalent)

GDP.1: 17 residues within 4Å: Chain A: N.27, F.33, F.37, V.47, R.49, Y.92, K.94, L.95, G.97, P.99, G.204, H.205, M.207, I.218, D.219 Ligands: MG.2, MG.3 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:N.27, A:L.95, A:L.95, A:G.97, A:D.219, A:D.219 Water bridges: A:R.49, A:R.49, A:Y.92, A:H.205, A:D.219 Salt bridges: A:R.49

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: D.219, T.221 Ligands: GDP.1 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.219, A:T.221, H2O.1, H2O.3, H2O.4 MG.3: 3 residues within 4Å: Chain A: H.205, D.219 Ligands: GDP.1 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.205, A:D.219, H2O.6, H2O.7

1 x CTY: CLARITHROMYCIN(Non-covalent)

CTY.4: 18 residues within 4Å: Chain A: I.103, G.108, N.109, Y.110, D.200, V.201, H.202, E.222, H.230, I.233, F.234, R.237, A.238, S.276, I.277, F.280, Y.289, M.292 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:I.103, A:Y.110, A:I.233, A:F.234, A:R.237, A:R.237, A:F.280 Hydrogen bonds: A:H.202, A:S.276 Water bridges: A:R.237 Salt bridges: A:D.200, A:E.222, A:R.237

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fong, D.H. et al., Structural Basis for Kinase-Mediated Macrolide Antibiotic Resistance. Structure (2017)

Release Date

2017-04-26

Peptides

Macrolide 2'-phosphotransferase II: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Macrolide 2'-phosphotransferase II

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