SMTL ID : 3dr4.1 (1 other biounit)

GDP-perosamine synthase K186A mutant from Caulobacter crescentus with bound sugar ligand

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

2 x G4M: [(2R,3S,4R,5R)-5-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2R,3S,4S,5S,6R)-3,4-dihydroxy-5-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)amino]-6-methyltetrahydro-2H-pyran-2-yl dihydrogen diphosphate(Non-covalent)

G4M.1: 30 residues within 4Å: Chain A: S.28, A.30, P.32, N.79, G.80, T.81, L.84, T.105, Y.106, A.108, V.151, D.177, A.179, E.180, S.201, F.203, G.204, N.205, W.306, E.333, R.335, F.338 Chain B: T.49, W.50, I.51, S.52, V.54, R.240, Y.241, N.249 41 PLIP interactions: 26 interactions with chain A, 15 interactions with chain B Hydrophobic interactions: A:Y.106, A:Y.106, A:Y.106, A:V.151, A:A.179, A:W.306, A:F.338 Hydrogen bonds: A:N.79, A:G.80, A:T.81, A:T.81, A:E.180, A:E.180, A:S.201, A:N.205, A:E.333, B:T.49, B:T.49, B:I.51, B:S.52, B:S.52, B:Q.233, B:N.249 Water bridges: A:S.28, A:S.28, A:S.28, A:Y.106, A:Y.106, A:S.201, A:N.205, A:R.335, B:T.49, B:R.240, B:R.251, B:R.251 Salt bridges: A:R.335, A:R.335, B:R.240, B:R.240 pi-Stacking: B:W.50 pi-Cation interactions: B:W.50 G4M.2: 29 residues within 4Å: Chain A: T.49, W.50, I.51, S.52, V.54, R.240, Y.241, N.249 Chain B: V.29, A.30, P.32, N.79, G.80, T.81, L.84, Y.106, A.108, V.151, D.177, A.179, E.180, S.201, F.203, G.204, N.205, W.306, E.333, R.335, F.338 36 PLIP interactions: 21 interactions with chain B, 15 interactions with chain A Hydrophobic interactions: B:Y.106, B:V.151, B:A.179, B:W.306, B:F.338 Hydrogen bonds: B:A.30, B:G.80, B:T.81, B:T.81, B:E.180, B:E.180, B:S.201, B:N.205, B:E.333, A:T.49, A:T.49, A:I.51, A:S.52, A:S.52, A:Q.233, A:Y.241, A:N.249 Water bridges: B:S.28, B:S.28, B:Y.106, B:S.201, B:N.205, A:R.251, A:R.251, A:R.251 Salt bridges: B:R.335, B:R.335, A:R.240, A:R.240 pi-Stacking: A:W.50 pi-Cation interactions: A:W.50

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

EDO.3: 8 residues within 4Å: Chain B: L.312, G.313, L.316, T.318, R.320, V.363, D.364 Ligands: EDO.4 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.318, B:V.363 EDO.4: 5 residues within 4Å: Chain B: L.316, S.317, T.318, T.319 Ligands: EDO.3 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:L.316

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
A

B
B

Putative perosamine synthetase

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