SMTL ID : 2wk1.1

Structure of the O-methyltransferase NovP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

homo-dimer

Ligands

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

SAH.1: 22 residues within 4Å: Chain A: T.84, M.85, I.86, E.112, G.114, V.115, W.116, A.120, D.142, S.143, G.146, I.147, P.148, L.170, G.196, W.197, F.198, R.214, D.216, G.217, D.218, S.222 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:W.116 Hydrogen bonds: A:M.85, A:G.114, A:V.115, A:W.116, A:A.120, A:S.143, A:G.146, A:F.198, A:R.214, A:D.216, A:S.222, A:S.222 Water bridges: A:G.118, A:G.118, A:F.144, A:F.144, A:K.199, A:E.221, A:D.225 pi-Stacking: A:F.198 SAH.6: 22 residues within 4Å: Chain B: T.84, M.85, I.86, E.112, G.114, V.115, W.116, A.120, D.142, S.143, G.146, I.147, P.148, L.170, G.196, W.197, F.198, R.214, D.216, G.217, D.218, S.222 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:W.116 Hydrogen bonds: B:T.84, B:M.85, B:G.114, B:V.115, B:W.116, B:A.120, B:S.143, B:G.146, B:F.198, B:R.214, B:S.222, B:S.222 Water bridges: B:G.118, B:G.118, B:F.144, B:F.144, B:K.199 pi-Stacking: B:F.198

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

SO4.2: 2 residues within 4Å: Chain A: H.164, R.165 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:H.164, A:R.165 SO4.3: 3 residues within 4Å: Chain A: R.76, M.247, R.273 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.76, A:R.273 SO4.7: 2 residues within 4Å: Chain B: H.164, R.165 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:H.164, B:R.165 SO4.8: 3 residues within 4Å: Chain B: R.76, M.247, R.273 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:R.76, B:R.273

4 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 1 residues within 4Å: Chain A: R.192 1 PLIP interactions: 1 interactions with chain A Water bridges: A:F.193 EDO.5: 8 residues within 4Å: Chain A: M.215, D.216, G.217, T.223, V.242, D.243, D.244, C.251 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:G.217, A:D.218, A:D.243, A:D.244, A:D.244 Water bridges: A:D.216, A:S.222 EDO.9: 1 residues within 4Å: Chain B: R.192 1 PLIP interactions: 1 interactions with chain B Water bridges: B:F.193 EDO.10: 8 residues within 4Å: Chain B: M.215, D.216, G.217, T.223, V.242, D.243, D.244, C.251 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:G.217, B:D.218, B:D.243, B:D.244, B:D.244 Water bridges: B:D.216, B:S.222, B:D.243

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gomez Garcia, I. et al., The Crystal Structure of the Novobiocin Biosynthetic Enzyme Novp: The First Representative Structure for the Tylf O-Methyltransferase Superfamily. J.Mol.Biol. (2010)

Release Date

2009-12-15

Peptides

NOVP: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

NOVP