SMTL ID : 4f97.1

Crystal Structure of VldE, the pseudo-glycosyltransferase, in complex with GDP and validoxylamine A 7'-phosphate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.11 Å

Oligo State

homo-dimer

Ligands

2 x GDP: GUANOSINE-5'-DIPHOSPHATE(Non-covalent)

GDP.1: 15 residues within 4Å: Chain A: R.290, K.295, R.321, N.323, D.360, N.361, D.362, V.363, T.366, D.383, N.386, L.387, S.388, E.391 Ligands: VDO.2 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:R.321, A:N.323, A:N.361, A:N.361, A:D.362, A:T.366, A:N.386, A:L.387, A:S.388, A:E.391 Water bridges: A:N.386, A:S.388 Salt bridges: A:R.290, A:K.295, A:K.295 GDP.6: 15 residues within 4Å: Chain B: R.290, K.295, R.321, N.323, D.360, N.361, D.362, V.363, T.366, D.383, N.386, L.387, S.388, E.391 Ligands: VDO.5 19 PLIP interactions: 19 interactions with chain B Hydrogen bonds: B:R.321, B:N.323, B:N.361, B:N.361, B:D.362, B:T.366, B:N.386, B:N.386, B:L.387, B:S.388, B:E.391 Water bridges: B:N.361, B:V.363, B:V.363, B:N.386, B:S.388 Salt bridges: B:R.290, B:K.295, B:K.295

2 x VDO: [(1R,2R,3S,4S,5S)-2,3,4-TRIHYDROXY-5-{[(1S,4R,5S,6S)-4,5,6-TRIHYDROXY-3-(HYDROXYMETHYL)CYCLOHEX-2-EN-1-YL]AMINO}CYCLOHEXYL]METHYL DIHYDROGEN PHOSPHATE(Non-covalent)

VDO.2: 16 residues within 4Å: Chain A: W.105, D.158, Y.159, Q.160, H.182, I.183, F.215, R.290, N.325, R.326, D.383, G.384, Q.385, N.386, L.387 Ligands: GDP.1 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:H.182, A:F.215 Hydrogen bonds: A:D.158, A:Q.160, A:R.290, A:N.325, A:D.383, A:D.383, A:G.384, A:Q.385, A:N.386, A:L.387 Salt bridges: A:R.326 VDO.5: 16 residues within 4Å: Chain B: W.105, D.158, Y.159, Q.160, H.182, I.183, F.215, R.290, N.325, R.326, D.383, G.384, Q.385, N.386, L.387 Ligands: GDP.6 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:H.182, B:F.215 Hydrogen bonds: B:D.158, B:Q.160, B:H.182, B:R.290, B:N.325, B:D.383, B:Q.385, B:N.386, B:L.387 Water bridges: B:G.384, B:G.384 Salt bridges: B:K.11, B:R.326

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

EDO.3: 7 residues within 4Å: Chain A: R.218, W.219, E.406, T.407, C.408, G.409, E.412 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.218, A:T.407, A:E.412 Water bridges: A:R.218, A:R.221, A:E.412 EDO.7: 6 residues within 4Å: Chain B: R.218, W.219, E.406, T.407, C.408, E.412 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.218, B:T.407, B:E.412 Water bridges: B:R.221

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 7 residues within 4Å: Chain A: Y.110, S.187, Y.190 Chain B: R.114, D.189, Y.190 Ligands: CL.8 Ligand excluded by PLIP CL.8: 6 residues within 4Å: Chain A: R.114, D.189, Y.190 Chain B: Y.110, S.187 Ligands: CL.4 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cavalier, M.C. et al., Mechanistic Insights into Validoxylamine A 7'-Phosphate Synthesis by VldE Using the Structure of the Entire Product Complex. Plos One (2012)

Release Date

2012-10-17

Peptides

VldE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

VldE

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