SMTL ID : 5u4t.1

Crystal structure of a methyltransferase involved in the biosynthesis of gentamicin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.09 Å

Oligo State

monomer

Ligands

13 x IOD: IODIDE ION(Non-functional Binders)

IOD.1: 5 residues within 4Å: Chain A: M.179, F.180, T.216, N.220, R.223 Ligand excluded by PLIP IOD.2: 3 residues within 4Å: Chain A: T.6, I.7, R.155 Ligand excluded by PLIP IOD.3: 3 residues within 4Å: Chain A: P.9, E.10, R.161 Ligand excluded by PLIP IOD.4: 3 residues within 4Å: Chain A: R.161, R.175, E.176 Ligand excluded by PLIP IOD.5: 3 residues within 4Å: Chain A: R.161, T.173, F.174 Ligand excluded by PLIP IOD.6: 2 residues within 4Å: Chain A: P.289, V.290 Ligand excluded by PLIP IOD.7: 3 residues within 4Å: Chain A: V.2, R.80, P.93 Ligand excluded by PLIP IOD.8: 4 residues within 4Å: Chain A: V.69, S.76, S.77, P.78 Ligand excluded by PLIP IOD.9: 3 residues within 4Å: Chain A: F.203, A.209, I.213 Ligand excluded by PLIP IOD.10: 4 residues within 4Å: Chain A: Q.83, L.84, H.85, G.86 Ligand excluded by PLIP IOD.11: 2 residues within 4Å: Chain A: Q.268, R.269 Ligand excluded by PLIP IOD.12: 2 residues within 4Å: Chain A: H.101, R.102 Ligand excluded by PLIP IOD.13: 4 residues within 4Å: Chain A: R.246, E.247, A.250, L.292 Ligand excluded by PLIP

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

SAH.14: 30 residues within 4Å: Chain A: D.106, L.108, A.111, L.114, D.128, M.129, G.130, C.131, G.132, S.133, G.134, V.135, L.136, V.150, D.151, V.152, N.153, A.156, G.177, D.178, M.179, F.192, N.193, S.194, P.195, L.206, L.207, A.209, I.213 Ligands: TRS.15 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:D.106 Hydrogen bonds: A:G.130, A:G.130, A:G.132, A:D.151, A:D.151, A:V.152, A:D.178, A:D.178, A:M.179, A:N.193 Water bridges: A:G.134

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.15: 12 residues within 4Å: Chain A: D.106, W.109, E.110, N.193, S.194, P.195, T.196, N.197, L.207, N.234, R.280 Ligands: SAH.14 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.110, A:N.193, A:N.193, A:T.196 Water bridges: A:D.106, A:D.106

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