SMTL ID : 4pzf.6 (5 other biounits)

Berberine bridge enzyme G164A variant, a reticuline dehydrogenase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

2 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 6 residues within 4Å: Chain A: N.38, R.52, F.53, L.56, L.76, N.124 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.56 Hydrogen bonds: A:R.52, A:R.52 NAG-NAG.2: 6 residues within 4Å: Chain B: N.38, R.52, F.53, L.56, L.76, N.124 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:F.53, B:L.56 Hydrogen bonds: B:R.52

2 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, A.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, H.459 28 PLIP interactions: 28 interactions with chain A Hydrophobic interactions: A:H.104, A:Y.106, A:V.169 Hydrogen bonds: A:L.99, 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:H.174, A:F.180, A:F.180, A:G.226, A:I.231, A:I.231, A:Y.456, A:N.458, A:N.458 Water bridges: A:Y.106, A:V.227 FAD.6: 28 residues within 4Å: Chain B: L.99, R.100, S.101, G.102, G.103, H.104, S.105, Y.106, S.110, L.122, S.141, A.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 27 PLIP interactions: 27 interactions with chain B Hydrophobic interactions: B:Y.106, B:V.169 Hydrogen bonds: B:L.99, B:S.101, B:G.102, B:G.103, B:H.104, B:S.105, B:S.110, B:S.110, B:S.141, B:W.165, B:G.170, B:G.170, B:G.173, B:H.174, B:F.180, B:F.180, B:G.226, B:I.231, B:I.231, B:N.458, B:N.458 Water bridges: B:Y.106, B:G.225, B:V.227 pi-Cation interactions: B:H.174

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

NAG.4: 2 residues within 4Å: Chain A: N.471, V.474 No protein-ligand interaction detected (PLIP) NAG.7: 3 residues within 4Å: Chain B: N.471, T.473, V.474 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.471

3 x SO4: SULFATE ION(Non-functional Binders)

SO4.5: 4 residues within 4Å: Chain A: G.35, R.37 Chain B: R.88, K.92 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Salt bridges: A:R.37, B:R.88, B:K.92 SO4.9: 5 residues within 4Å: Chain B: Y.187, D.192, N.193, Q.395, I.399 No protein-ligand interaction detected (PLIP) SO4.10: 3 residues within 4Å: Chain B: R.209, R.221, F.403 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:R.209, B:R.221

1 x 12P: DODECAETHYLENE GLYCOL(Non-covalent)

12P.8: 11 residues within 4Å: Chain A: K.80, W.138, I.206, D.208 Chain B: K.80, S.129, W.138, E.140, I.206, D.208, Y.232 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.127

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zafred, D. et al., Rationally engineered flavin-dependent oxidase reveals steric control of dioxygen reduction. Febs J. (2015)

Release Date

2014-04-23

Peptides

Reticuline oxidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
D

Reticuline oxidase

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