SMTL ID : 3ng7.1

Complex of dithionite-reduced 6-hydroxy-L-nicotine oxidase with substrate bound at active site and inhibitor at exit cavity

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-dimer

Ligands

2 x HNL: 5-[(2S)-1-methylpyrrolidin-2-yl]pyridin-2-ol(Non-covalent)

HNL.1: 11 residues within 4Å: Chain A: Y.59, W.163, N.166, M.167, L.198, Y.311, F.326, W.371, G.406, Y.407 Ligands: FAD.2 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:Y.59, A:L.198, A:W.371 Hydrogen bonds: A:N.166, A:N.166, A:Y.311 Water bridges: A:Y.407 pi-Stacking: A:F.326 HNL.5: 11 residues within 4Å: Chain B: Y.59, W.163, N.166, M.167, L.198, Y.311, F.326, W.371, G.406, Y.407 Ligands: FAD.6 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:Y.59, B:L.198, B:W.371 Hydrogen bonds: B:N.166, B:N.166 pi-Stacking: B:F.326

2 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)

FAD.2: 36 residues within 4Å: Chain A: V.7, G.8, G.9, G.10, F.11, S.12, L.30, E.31, G.32, G.37, G.38, R.39, A.40, G.56, G.57, A.58, Y.59, T.224, V.225, V.226, A.254, T.255, P.256, K.287, W.361, L.366, F.367, P.370, W.371, G.397, S.398, G.406, Y.407, I.408, A.411 Ligands: HNL.1 35 PLIP interactions: 35 interactions with chain A Hydrophobic interactions: A:R.39, A:K.287, A:P.370, A:W.371 Hydrogen bonds: A:G.9, A:G.10, A:S.12, A:G.32, A:R.39, A:G.57, A:A.58, A:Y.59, A:Y.59, A:V.226, A:V.226, A:S.398, A:S.398, A:S.398, A:G.406, A:I.408 Water bridges: A:G.13, A:E.31, A:E.31, A:G.38, A:R.39, A:R.39, A:A.40, A:A.40, A:T.255, A:T.259, A:D.399, A:E.409 Salt bridges: A:R.39, A:R.39 pi-Stacking: A:W.371 FAD.6: 36 residues within 4Å: Chain B: V.7, G.8, G.9, G.10, F.11, S.12, L.30, E.31, G.32, G.37, G.38, R.39, A.40, G.56, G.57, A.58, Y.59, T.224, V.225, V.226, A.254, T.255, P.256, K.287, W.361, L.366, F.367, P.370, W.371, G.397, S.398, G.406, Y.407, I.408, A.411 Ligands: HNL.5 34 PLIP interactions: 34 interactions with chain B Hydrophobic interactions: B:R.39, B:K.287, B:P.370, B:W.371 Hydrogen bonds: B:G.9, B:G.10, B:S.12, B:G.32, B:R.39, B:G.57, B:A.58, B:Y.59, B:Y.59, B:V.226, B:V.226, B:T.259, B:S.398, B:S.398, B:S.398, B:G.406, B:I.408 Water bridges: B:F.11, B:G.13, B:E.31, B:E.31, B:G.38, B:R.39, B:R.39, B:A.40, B:D.399, B:E.409 Salt bridges: B:R.39, B:R.39 pi-Stacking: B:W.371

2 x GP7: (1R)-2-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(pentadecanoyloxy)methyl]ethyl (12E)-hexadeca-9,12-dienoate(Non-covalent)

GP7.3: 16 residues within 4Å: Chain A: F.101, T.115, F.159, L.160, W.163, A.164, M.180, I.191, L.192, V.195 Chain B: V.97, F.101, I.103, P.104, G.105, A.108 14 PLIP interactions: 8 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:F.101, A:F.159, A:L.160, A:W.163, A:I.191, A:L.192, A:V.195, B:F.101 Water bridges: A:Q.99, B:Q.99, B:Q.99, B:S.106 Hydrogen bonds: B:I.103, B:G.105 GP7.7: 16 residues within 4Å: Chain A: V.97, F.101, I.103, P.104, G.105, A.108 Chain B: F.101, T.115, F.159, L.160, W.163, A.164, M.180, I.191, L.192, V.195 14 PLIP interactions: 8 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:F.101, B:F.159, B:L.160, B:W.163, B:I.191, B:L.192, B:V.195, A:F.101 Water bridges: B:Q.99, A:Q.99, A:Q.99, A:S.106 Hydrogen bonds: A:I.103, A:G.105

2 x HNK: 5-[(2R)-1-methylpyrrolidin-2-yl]pyridin-2-ol(Non-covalent)

HNK.4: 8 residues within 4Å: Chain A: Y.59, A.82, S.83, F.85, V.195, L.198, Y.311, D.312 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:Y.59, A:A.82, A:F.85, A:V.195, A:L.198, A:Y.311 Hydrogen bonds: A:S.83, A:S.83 pi-Stacking: A:F.85 HNK.8: 8 residues within 4Å: Chain B: Y.59, A.82, S.83, F.85, V.195, L.198, Y.311, D.312 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:Y.59, B:A.82, B:F.85, B:V.195, B:L.198, B:Y.311 Hydrogen bonds: B:Y.59, B:S.83, B:S.83 Water bridges: B:D.199 pi-Stacking: B:F.85

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kachalova, G. et al., Crystallographic snapshots of the complete reaction cycle of nicotine degradation by an amine oxidase of the monoamine oxidase (MAO) family. Proc.Natl.Acad.Sci.USA (2011)

Release Date

2011-03-16

Peptides

6-hydroxy-L-nicotine oxidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
X

B
X

6-hydroxy-L-nicotine oxidase

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