SMTL ID : 3gsy.1

Structure of berberine bridge enzyme in complex with dehydroscoulerine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.63 Å

Oligo State

monomer

Ligands

1 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Covalent)

NAG-NAG-BMA.1: 6 residues within 4Å: Chain A: N.19, R.33, F.34, L.37, L.57, N.105 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.37 Hydrogen bonds: A:R.33

1 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Covalent)

FAD.2: 29 residues within 4Å: Chain A: L.80, R.81, S.82, G.83, G.84, H.85, S.86, Y.87, S.91, L.103, S.122, G.145, W.146, C.147, V.150, G.151, G.153, G.154, H.155, G.160, F.161, G.206, G.207, G.210, A.211, I.212, Y.437, N.439 Ligands: DEH.3 30 PLIP interactions: 30 interactions with chain A Hydrophobic interactions: A:H.85, A:Y.87, A:V.150 Hydrogen bonds: A:L.80, A:S.82, A:G.83, A:G.84, A:H.85, A:S.86, A:S.91, A:S.91, A:S.122, A:W.146, A:C.147, A:G.151, A:G.151, A:G.154, A:H.155, A:F.161, A:F.161, A:G.207, A:I.212, A:I.212, A:N.439, A:N.439, A:N.439 Water bridges: A:Y.87, A:G.206, A:V.208, A:H.493

1 x DEH: 2,9-dihydroxy-3,10-dimethoxy-5,6-dihydroisoquino[3,2-a]isoquinolinium(Non-covalent)

DEH.3: 11 residues within 4Å: Chain A: Y.87, W.146, M.163, S.261, L.263, D.333, F.337, F.367, N.371, E.398 Ligands: FAD.2 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:W.146, A:W.146, A:W.146, A:L.263 Hydrogen bonds: A:D.333, A:N.371 Water bridges: A:R.335

1 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.4: 3 residues within 4Å: Chain A: N.452, T.454, V.455 3 PLIP interactions: 3 interactions with chain A Water bridges: A:N.452, A:N.452, A:N.452

1 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 2 residues within 4Å: Chain A: D.26, D.28 6 PLIP interactions: 2 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.26, A:D.28, H2O.1, H2O.1, H2O.1, H2O.2

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Winkler, A. et al., Berberine bridge enzyme catalyzes the six electron oxidation of (S)-reticuline to dehydroscoulerine. Phytochemistry (2009)

Release Date

2009-06-30

Peptides

Reticuline oxidase; Berberine bridge-forming enzyme: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Reticuline oxidase; Berberine bridge-forming enzyme