SMTL ID : 2x0e.1

Complex structure of WsaF with dTDP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.81 Å

Oligo State

homo-dimer

Ligands

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

TYD.1: 11 residues within 4Å: Chain A: F.62, G.63, Y.247, R.249, G.283, K.302, L.303, L.305, Y.308, Y.329, E.333 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:Y.247, A:L.305, A:Y.308 Hydrogen bonds: A:G.63, A:Y.247, A:K.302, A:L.303, A:L.303 Water bridges: A:R.249 Salt bridges: A:R.249, A:R.249, A:K.302 pi-Stacking: A:Y.308 pi-Cation interactions: A:K.302 TYD.4: 12 residues within 4Å: Chain B: F.62, G.63, Y.247, R.249, V.282, G.283, K.302, L.303, L.305, Y.308, Y.329, E.333 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:V.282, B:Y.308, B:Y.308 Hydrogen bonds: B:G.63, B:K.302, B:L.303, B:L.303 Water bridges: B:E.333 Salt bridges: B:R.249, B:R.249, B:K.302 pi-Stacking: B:Y.308 pi-Cation interactions: B:K.302

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 2 residues within 4Å: Chain A: Y.220, F.221 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.221, A:F.221 GOL.3: 7 residues within 4Å: Chain A: F.172, Y.183, Y.208, E.347 Chain B: F.172, Y.183 Ligands: GOL.5 8 PLIP interactions: 3 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:Y.183, A:Y.183, A:Y.183, A:E.347, A:E.347 Water bridges: B:Y.183, B:Y.208, A:Y.346 GOL.5: 12 residues within 4Å: Chain A: G.175, Y.177, Q.178, W.179, Y.183 Chain B: P.174, G.175, Y.177, Q.178, W.179, Y.183 Ligands: GOL.3 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:G.175, B:W.179, B:W.179

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Steiner, K. et al., Structural Basis of Substrate Binding in Wsaf, a Rhamnosyltransferase from Geobacillus Stearothermophilus. J.Mol.Biol. (2010)

Release Date

2010-02-02

Peptides

WSAF: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

WSAF

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