SMTL ID : 3dr7.2 (1 other biounit)

GDP-perosamine synthase from Caulobacter crescentus with bound GDP-3-deoxyperosamine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

2 x GPD: (2R,3S,5S,6R)-5-amino-3-hydroxy-6-methyl-oxan-2-yl(Non-covalent)

GPD.1: 18 residues within 4Å: Chain A: S.28, V.29, A.30, P.32, Y.106, F.203, G.204, N.205, K.206, W.306, E.333, R.335 Chain B: T.49, W.50, I.51, S.52, R.240, Y.241 19 PLIP interactions: 10 interactions with chain B, 9 interactions with chain A Hydrogen bonds: B:T.49, B:T.49, B:I.51, B:S.52, B:S.52, B:R.240, A:N.205, A:E.333 Water bridges: B:T.49, A:S.28, A:S.28, A:Y.106 Salt bridges: B:R.240, A:R.335, A:R.335 pi-Stacking: B:W.50 pi-Cation interactions: B:W.50 Hydrophobic interactions: A:F.203, A:W.306 GPD.2: 18 residues within 4Å: Chain A: T.49, W.50, I.51, S.52, R.240 Chain B: S.28, V.29, A.30, P.32, Y.106, F.203, G.204, N.205, K.206, W.306, E.333, R.335, F.338 17 PLIP interactions: 9 interactions with chain A, 8 interactions with chain B Hydrogen bonds: A:T.49, A:T.49, A:I.51, A:S.52, A:S.52, B:E.333, B:R.335 Salt bridges: A:R.240, A:R.240, B:R.335 pi-Stacking: A:W.50 pi-Cation interactions: A:W.50 Hydrophobic interactions: B:Y.106, B:W.306, B:F.338 Water bridges: B:Y.106, B:Y.106

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

EDO.3: 4 residues within 4Å: Chain B: R.128, T.293, K.294, H.296 2 PLIP interactions: 2 interactions with chain B Water bridges: B:P.127, B:H.296

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cook, P.D. et al., Accommodation of GDP-linked sugars in the active site of GDP-perosamine synthase. Biochemistry (2008)

Release Date

2008-10-14

Peptides

Putative perosamine synthetase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

Putative perosamine synthetase

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