SMTL ID : 3m9v.1

X-ray Structure of a KijD3 in Complex with dTDP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

homo-tetramer

Ligands

4 x TYD: THYMIDINE-5'-DIPHOSPHATE(Non-covalent)

TYD.1: 12 residues within 4Å: Chain A: T.111, Y.114, E.115, N.184, R.242, V.252, A.254, G.255, Q.256, V.258, S.259, R.332 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:Y.114 Hydrogen bonds: A:E.115, A:N.184, A:R.242, A:Q.256, A:S.259, A:R.332, A:R.332 pi-Stacking: A:Y.114 TYD.2: 12 residues within 4Å: Chain B: T.111, Y.114, E.115, N.184, R.242, V.252, A.254, G.255, Q.256, V.258, S.259, R.332 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:Y.114 Hydrogen bonds: B:E.115, B:N.184, B:R.242, B:Q.256, B:S.259, B:R.332, B:R.332 pi-Stacking: B:Y.114 TYD.3: 12 residues within 4Å: Chain C: T.111, Y.114, E.115, N.184, R.242, V.252, A.254, G.255, Q.256, V.258, S.259, R.332 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:Y.114 Hydrogen bonds: C:N.184, C:R.242, C:Q.256, C:S.259, C:R.332, C:R.332 pi-Stacking: C:Y.114 TYD.4: 12 residues within 4Å: Chain D: T.111, Y.114, E.115, N.184, R.242, V.252, A.254, G.255, Q.256, V.258, S.259, R.332 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:Y.114 Hydrogen bonds: D:N.184, D:R.242, D:Q.256, D:S.259, D:R.332, D:R.332 pi-Stacking: D:Y.114

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bruender, N.A. et al., X-ray structure of kijd3, a key enzyme involved in the biosynthesis of D-kijanose. Biochemistry (2010)

Release Date

2010-04-07

Peptides

FAD-dependent oxidoreductase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

FAD-dependent oxidoreductase