SMTL ID : 5n5d.1

Crystal Structure of the O-Methyltransferase TomG from Streptomyces achromogenes involved in Tomaymycin synthesis in complex with SAM

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

homo-dimer

Ligands

5 x BU3: (R,R)-2,3-BUTANEDIOL(Non-covalent)

BU3.1: 10 residues within 4Å: Chain A: V.45, Q.49, L.52, L.53, L.56, F.141, V.167, D.169, F.219 Chain B: I.208 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.52, A:L.53, A:F.141, A:V.167, A:D.169 Hydrogen bonds: A:D.169 Water bridges: A:N.170 BU3.2: 4 residues within 4Å: Chain A: D.179, D.181, H.182, P.183 No protein-ligand interaction detected (PLIP) BU3.3: 7 residues within 4Å: Chain A: S.18, S.19, V.22, K.23, E.24, A.47, P.48 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:E.24 Hydrogen bonds: A:S.18, A:S.18 Water bridges: A:S.18, A:S.19 BU3.9: 10 residues within 4Å: Chain A: I.208 Chain B: V.45, Q.49, L.52, L.53, L.56, F.141, V.167, D.169, F.219 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:L.52, B:L.53, B:F.141, B:D.169 Water bridges: B:N.170 BU3.10: 7 residues within 4Å: Chain B: S.18, S.19, V.22, K.23, E.24, A.47, P.48 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:E.24 Hydrogen bonds: B:S.18 Water bridges: B:S.18, B:S.19

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 6 residues within 4Å: Chain A: L.173, G.174, A.176, H.182, D.184, V.187 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.184 GOL.5: 4 residues within 4Å: Chain A: M.5, E.6, Q.7, R.9 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.6

2 x SAM: S-ADENOSYLMETHIONINE(Non-covalent)

SAM.6: 24 residues within 4Å: Chain A: L.43, A.44, V.45, E.67, G.69, T.70, F.71, G.73, Y.74, S.75, I.92, E.93, W.94, E.95, F.98, G.120, R.121, A.122, L.123, F.141, D.143, A.144, N.145, Y.152 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:F.71 Hydrogen bonds: A:V.45, A:E.67, A:F.71, A:Y.74, A:S.75, A:E.93, A:W.94, A:A.122, A:N.145 Water bridges: A:T.70, A:G.73, A:R.121, A:R.121, A:R.121, A:N.145, A:D.148 Salt bridges: A:D.143 SAM.11: 23 residues within 4Å: Chain B: L.43, A.44, V.45, E.67, G.69, T.70, F.71, Y.74, S.75, I.92, E.93, W.94, E.95, F.98, G.120, R.121, A.122, L.123, F.141, D.143, A.144, N.145, Y.152 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:F.71 Hydrogen bonds: B:V.45, B:G.69, B:F.71, B:Y.74, B:S.75, B:S.75, B:W.94, B:A.122, B:D.143, B:D.143, B:N.145, B:N.145 Water bridges: B:G.73, B:D.148, B:D.148, B:D.169 Salt bridges: B:D.143

5 x SO4: SULFATE ION(Non-functional Binders)

SO4.7: 3 residues within 4Å: Chain A: H.35, R.36, D.42 3 PLIP interactions: 3 interactions with chain A Water bridges: A:D.42 Salt bridges: A:H.35, A:R.36 SO4.8: 3 residues within 4Å: Chain A: N.145, K.146, P.147 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.146 Water bridges: A:A.144, A:N.145, A:K.146 Salt bridges: A:K.146 SO4.12: 3 residues within 4Å: Chain B: N.145, K.146, P.147 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:K.146 Water bridges: B:K.146, B:K.146, B:D.184, B:G.186 Salt bridges: B:K.146 SO4.13: 4 residues within 4Å: Chain B: Q.33, H.35, R.36, D.42 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:H.35, B:R.36 SO4.14: 2 residues within 4Å: Chain B: R.96, V.119 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.96

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

von Tesmar, A. et al., Total Biosynthesis of the Pyrrolo[4,2]benzodiazepine Scaffold Tomaymycin on an In Vitro Reconstituted NRPS System. Cell Chem Biol (2017)

Release Date

2017-09-20

Peptides

Methyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Methyltransferase