SMTL ID : 5u0t.1

Crystal structure of a methyltransferase involved in the biosynthesis of gentamicin in complex with (1R,2S,3S,4R,6S)-4,6-diamino-3-{[3-deoxy-3-(methylamino)-alpha-D-glucopyranosyl]oxy}-2-hydroxycyclohexyl 2,6-diamino-2,6-dideoxy-alpha-D-glucopyranoside

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.11 Å

Oligo State

monomer

Ligands

1 x SAH: S-ADENOSYL-L-HOMOCYSTEINE(Non-covalent)

SAH.1: 19 residues within 4Å: Chain A: D.127, D.149, G.151, C.152, G.153, V.156, L.157, D.172, V.173, N.174, G.198, D.199, M.200, N.214, P.216, L.227, L.228, I.234 Ligands: 7QM.2 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:G.151, A:G.151, A:G.153, A:V.173, A:D.199, A:D.199, A:M.200, A:N.214 Water bridges: A:L.129, A:G.155, A:N.174

1 x 7QM: (1R,2S,3S,4R,6S)-4,6-diamino-3-{[3-deoxy-3-(methylamino)-alpha-D-glucopyranosyl]oxy}-2-hydroxycyclohexyl 2,6-diamino-2,6-dideoxy-alpha-D-glucopyranoside(Non-covalent)

7QM.2: 16 residues within 4Å: Chain A: D.115, V.116, E.118, D.127, W.130, E.131, N.214, S.215, P.216, T.217, N.218, L.228, E.229, N.255, R.301 Ligands: SAH.1 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:W.130 Hydrogen bonds: A:V.116, A:E.118, A:E.131, A:E.131, A:S.215, A:N.218, A:L.228, A:E.229, A:N.255 Water bridges: A:E.118, A:N.214, A:N.214, A:R.301, A:R.301 Salt bridges: A:R.301

1 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain A: E.118, Q.121, D.226 6 PLIP interactions: 2 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:E.118, A:D.226, H2O.1, H2O.3, H2O.3, H2O.5

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bury, P.D.S. et al., Structural Basis of the Selectivity of GenN, an Aminoglycoside N-Methyltransferase Involved in Gentamicin Biosynthesis. ACS Chem. Biol. (2017)

Release Date

2017-11-01

Peptides

Putative gentamicin methyltransferase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Putative gentamicin methyltransferase

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