SMTL ID : 3d2d.1

Structure of berberine bridge enzyme in complex with (S)-reticuline

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

monomer

Ligands

1 x NAG- NAG- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-MAN-MAN-MAN-MAN.1: 8 residues within 4Å: Chain A: N.38, R.52, F.53, L.56, L.76, M.123, N.124, F.348 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.56, A:F.348 Hydrogen bonds: A:R.52

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

NAG.2: 3 residues within 4Å: Chain A: N.471, T.473, V.474 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.471

1 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Covalent)

FAD.3: 30 residues within 4Å: Chain A: L.99, R.100, S.101, G.102, G.103, H.104, S.105, Y.106, L.109, S.110, L.122, S.141, G.164, W.165, C.166, V.169, G.170, G.172, G.173, H.174, F.180, G.225, G.226, G.229, A.230, I.231, Y.456, N.458, H.459 Ligands: REN.4 27 PLIP interactions: 27 interactions with chain A Hydrophobic interactions: A:H.104, A:Y.106, A:V.169 Hydrogen bonds: A:L.99, A:S.101, A:G.102, A:G.103, A:H.104, A:H.104, A:S.105, A:L.109, A:S.110, A:S.110, A:S.141, A:W.165, A:G.170, A:G.170, A:G.173, A:F.180, A:F.180, A:G.226, A:I.231, A:I.231, A:N.458, A:H.459 Water bridges: A:V.227 pi-Stacking: A:H.174

1 x REN: (S)-reticuline(Non-covalent)

REN.4: 14 residues within 4Å: Chain A: Y.106, W.165, S.280, L.282, L.295, D.352, R.354, F.356, F.386, A.388, N.390, E.417, A.421 Ligands: FAD.3 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:W.165, A:L.282, A:F.356, A:A.388 Hydrogen bonds: A:Y.106, A:R.354, A:N.390 Water bridges: A:E.417 Salt bridges: A:E.417 pi-Stacking: A:F.386

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Winkler, A. et al., A concerted mechanism for berberine bridge enzyme. Nat.Chem.Biol. (2008)

Release Date

2008-10-28

Peptides

berberine bridge-forming enzyme: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

berberine bridge-forming enzyme

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