SMTL ID : 5dm4.1

Crystal structure of the plantazolicin methyltransferase BpumL in complex with pentazolic desmethylPZN analog and SAH

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

monomer

Ligands

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

SAH.1: 17 residues within 4Å: Chain A: Q.16, F.19, R.40, G.66, G.68, D.89, S.90, S.91, T.110, D.111, I.112, H.128, C.130, L.133, F.134 Ligands: GOL.2, 5DA.3 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:G.68, A:S.90, A:S.91, A:D.111, A:I.112, A:H.128 Water bridges: A:Q.16, A:R.25, A:R.40, A:R.40, A:R.40, A:S.90, A:S.90, A:H.128 Salt bridges: A:R.40, A:H.128

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 8 residues within 4Å: Chain A: D.111, I.112, F.134, E.135, N.136, E.139, L.140 Ligands: SAH.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.135, A:E.135, A:N.136 Water bridges: A:E.139

1 x 5DA: 1-[(4S)-4-(4-{4-[4-(5,5'-dimethyl-2,4'-bi-1,3-oxazol-2'-yl)-1,3-thiazol-2-yl]-5-methyl-1,3-oxazol-2-yl}-1,3-thiazol-2-yl)-4-(methylamino)butyl]guanidine(Non-covalent)

5DA.3: 19 residues within 4Å: Chain A: F.19, Y.31, D.32, T.36, T.39, L.129, C.130, G.132, L.133, D.158, L.159, Y.179, I.180, Q.183, S.187, Q.245, Y.246, L.256 Ligands: SAH.1 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:F.19, A:T.39, A:L.129, A:Y.246, A:L.256 Hydrogen bonds: A:Y.31, A:L.129, A:G.132, A:Q.183, A:Q.183, A:S.187 Salt bridges: A:D.158 pi-Stacking: A:Y.246

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hao, Y. et al., Insights into methyltransferase specificity and bioactivity of derivatives of the antibiotic plantazolicin. Acs Chem.Biol. (2015)

Release Date

2015-09-23

Peptides

Methyltransferase domain family: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Methyltransferase domain family

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