SMTL ID : 4e32.1

X-ray Structure of the C-3'-Methyltransferase TcaB9 in Complex with S-Adenosyl-L-Homocysteine and dTDP-Sugar Substrate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.15, C.18, C.56, C.59 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.15, A:C.18, A:C.56, A:C.59

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

EDO.2: 3 residues within 4Å: Chain A: R.166, G.170, P.171 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.166, A:R.166 Water bridges: A:G.170 EDO.3: 4 residues within 4Å: Chain A: T.218, N.300, I.304, E.412 4 PLIP interactions: 4 interactions with chain A Water bridges: A:T.218, A:T.218, A:P.411, A:E.412

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

SAH.4: 21 residues within 4Å: Chain A: F.74, Y.78, Y.80, S.82, F.92, I.114, G.115, N.117, F.135, E.136, P.137, S.138, F.156, F.157, A.178, N.179, T.180, H.183, I.184, Y.186 Ligands: DWN.5 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:N.117 Hydrogen bonds: A:S.82, A:G.115, A:N.117, A:S.138, A:S.138, A:F.157, A:F.157, A:N.179, A:T.180 Water bridges: A:A.178, A:Y.186 pi-Stacking: A:F.74

1 x DWN: (2R,4S,6R)-4-amino-6-methyl-5-oxotetrahydro-2H-pyran-2-yl [(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)tetrahydrofuran-2-yl]methyl dihydrogen diphosphate(Non-covalent)

DWN.5: 28 residues within 4Å: Chain A: D.35, Y.78, Y.80, G.84, S.85, N.179, H.183, Y.224, E.226, H.227, H.256, Y.325, G.326, A.327, T.328, A.329, K.330, D.350, T.351, T.352, K.355, A.385, N.387, H.388, E.391, I.392, K.395 Ligands: SAH.4 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:Y.80, A:N.179, A:H.388 Hydrogen bonds: A:Y.80, A:Y.224, A:E.226, A:A.329, A:K.330, A:T.351, A:K.355, A:N.387, A:K.395 Water bridges: A:Y.325, A:K.330, A:T.351, A:K.355, A:E.391, A:K.395 Salt bridges: A:H.256, A:K.330, A:K.330, A:H.388

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bruender, N.A. et al., Probing the catalytic mechanism of a C-3'-methyltransferase involved in the biosynthesis of D-tetronitrose. Protein Sci. (2012)

Release Date

2012-04-25

Peptides

TcaB9: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

TcaB9

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