SMTL ID : 3bxo.1

Crystal Structure of Streptomyces venezuelae DesVI

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

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

SAM.1: 19 residues within 4Å: Chain A: Y.23, A.48, C.49, G.50, H.54, E.69, L.70, S.71, M.74, G.90, D.91, M.92, R.93, M.107, F.108, S.110, Y.113, L.114 Ligands: UPP.2 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:Y.23, A:A.48, A:L.70, A:S.71, A:D.91, A:M.92, A:R.93, A:M.107, A:S.110 Water bridges: A:M.107 Salt bridges: A:H.54 SAM.3: 18 residues within 4Å: Chain B: Y.23, A.48, C.49, G.50, H.54, E.69, L.70, S.71, M.74, G.90, D.91, M.92, R.93, M.107, F.108, S.110, Y.113 Ligands: UPP.4 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:A.48, B:L.70, B:D.91, B:D.91, B:M.92, B:M.107, B:S.110 Water bridges: B:T.51, B:G.52, B:R.93 Salt bridges: B:H.54

2 x UPP: PHENYL-URIDINE-5'-DIPHOSPHATE(Non-covalent)

UPP.2: 19 residues within 4Å: Chain A: Y.16, R.19, F.108, S.109, Y.113, W.142, W.143, T.147, F.148, A.149, W.152, S.154, R.167, S.169, S.171, M.180, I.202, R.231 Ligands: SAM.1 24 PLIP interactions: 24 interactions with chain A Hydrophobic interactions: A:W.142, A:W.152, A:I.202 Hydrogen bonds: A:Y.16, A:T.147, A:A.149, A:A.149, A:S.154, A:S.154, A:S.169, A:S.171, A:S.171 Water bridges: A:R.19, A:R.19, A:R.231 Salt bridges: A:R.19, A:R.19, A:R.167, A:R.167, A:R.231 pi-Stacking: A:F.108, A:W.143, A:W.143 pi-Cation interactions: A:R.231 UPP.4: 17 residues within 4Å: Chain B: Y.16, R.19, F.108, Y.113, W.142, W.143, T.147, F.148, A.149, W.152, S.154, R.167, S.169, S.171, M.180, R.231 Ligands: SAM.3 21 PLIP interactions: 21 interactions with chain B Hydrophobic interactions: B:W.142, B:W.152 Hydrogen bonds: B:T.147, B:A.149, B:A.149, B:S.154, B:S.154, B:S.169, B:S.171, B:S.171 Water bridges: B:R.19, B:R.231 Salt bridges: B:R.19, B:R.19, B:R.167, B:R.167, B:R.231 pi-Stacking: B:F.108, B:W.143, B:W.143 pi-Cation interactions: B:R.231

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

EDO.5: 3 residues within 4Å: Chain B: R.173, E.174, G.175 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.175

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Burgie, E.S. et al., Three-Dimensional Structure of DesVI from Streptomyces venezuelae: A Sugar N,N-Dimethyltransferase Required for dTDP-Desosamine Biosynthesis. Biochemistry (2008)

Release Date

2008-03-25

Peptides

N,N-dimethyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

N,N-dimethyltransferase