SMTL ID : 3d2h.1

Structure of berberine bridge enzyme from Eschscholzia californica, monoclinic crystal form

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 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: 7 residues within 4Å: Chain A: N.38, R.52, F.53, L.56, L.76, M.123, N.124 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.53, A:L.56 Hydrogen bonds: A:R.52, A:R.52

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

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

1 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Covalent)

FAD.3: 29 residues within 4Å: Chain A: L.99, R.100, S.101, G.102, G.103, H.104, S.105, Y.106, S.110, L.122, S.141, G.164, W.165, C.166, V.169, G.170, G.172, G.173, H.174, G.179, F.180, G.225, G.226, G.229, A.230, I.231, Y.456, N.458 Ligands: FSH.4 31 PLIP interactions: 31 interactions with chain A Hydrophobic interactions: A:H.104, A:Y.106, A:C.166, A:V.169 Hydrogen bonds: A:L.99, A:S.101, A:G.102, A:G.103, A:H.104, A:S.105, 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:N.458, A:N.458 Water bridges: A:Y.106, A:Y.106, A:G.225, A:V.227, A:H.512 pi-Stacking: A:H.174

1 x FSH: (2R,3S,4S)-5-[(4R)-6',7'-dimethyl-2,3',5-trioxo-1'H-spiro[imidazolidine-4,2'-quinoxalin]-4'(3'H)-yl]-2,3,4-trihydroxypentyl-adenosine diphosphate(Covalent)

FSH.4: 28 residues within 4Å: Chain A: L.99, R.100, S.101, G.102, G.103, H.104, S.105, Y.106, 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, N.458, H.459 Ligands: FAD.3 36 PLIP interactions: 36 interactions with chain A Hydrophobic interactions: A:H.104, A:Y.106, A:C.166, A:V.169 Hydrogen bonds: A:L.99, A:S.101, A:G.102, A:G.103, A:H.104, A:S.105, A:S.110, A:S.110, A:S.141, A:W.165, A:W.165, A:G.170, A:G.173, A:H.174, A:F.180, A:G.226, A:I.231, A:I.231, A:N.458, A:N.458 Water bridges: A:Y.106, A:Y.106, A:Y.106, A:W.165, A:W.165, A:F.180, A:G.225, A:V.227, A:N.390, A:E.417, A:N.458, A:H.512

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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