SMTL ID : 3nk0.1

Complex of 6-hydroxy-L-nicotine oxidase with inhibitor bound at active site and turnover product at exit cavity

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

homo-dimer

Ligands

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

HNK.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 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Y.59, A:L.198, A:Y.407 Hydrogen bonds: A:N.166, A:N.166, A:Y.311 pi-Stacking: A:F.326 HNK.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:Y.407 Hydrogen bonds: B:N.166, B:N.166 pi-Stacking: B:F.326

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

FAD.2: 37 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, T.259, 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: HNK.1 36 PLIP interactions: 36 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:A.40, 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:T.255, A:T.255, A:T.259, A:T.259, A:D.399, A:E.409 Salt bridges: A:R.39, A:R.39 pi-Stacking: A:W.371 FAD.6: 37 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, T.259, 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: HNK.5 35 PLIP interactions: 35 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:A.40, 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:F.11, B:G.13, B:E.31, B:E.31, B:G.38, B:R.39, B:R.39, 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: 21 residues within 4Å: Chain A: Q.99, A.100, F.101, T.115, F.159, L.160, W.163, A.164, M.180, I.191, L.192, V.194, V.195 Chain B: V.97, F.101, I.103, P.104, G.105, A.108, E.112 Ligands: GP7.7 18 PLIP interactions: 13 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:F.101, A:F.101, A:F.159, A:L.160, A:W.163, A:A.164, A:I.191, A:L.192, A:L.192, A:V.194, A:V.195, B:F.101, B:E.112 Water bridges: A:Q.99, A:Q.99, B:S.106 Hydrogen bonds: B:I.103, B:G.105 GP7.7: 21 residues within 4Å: Chain A: V.97, F.101, I.103, P.104, G.105, A.108, E.112 Chain B: Q.99, A.100, F.101, T.115, F.159, L.160, W.163, A.164, M.180, I.191, L.192, V.194, V.195 Ligands: GP7.3 18 PLIP interactions: 13 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:F.101, B:F.101, B:F.159, B:L.160, B:W.163, B:A.164, B:I.191, B:L.192, B:L.192, B:V.194, B:V.195, A:F.101, A:E.112 Water bridges: B:Q.99, B:Q.99, A:S.106 Hydrogen bonds: A:I.103, A:G.105

2 x HNM: 1-(6-hydroxypyridin-3-yl)-4-(methylamino)butan-1-one(Non-covalent)

HNM.4: 8 residues within 4Å: Chain A: Y.59, F.85, W.163, V.195, L.196, L.198, E.300, Y.311 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:W.163, A:V.195, A:L.196, A:L.198 Hydrogen bonds: A:L.198, A:L.198 pi-Stacking: A:F.85, A:Y.311 HNM.8: 8 residues within 4Å: Chain B: Y.59, F.85, W.163, V.195, L.196, L.198, E.300, Y.311 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:W.163, B:V.195, B:L.196, B:L.198 Hydrogen bonds: B:L.198, B:L.198 Water bridges: B:D.199 pi-Stacking: B:F.85, B:Y.311

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kachalova, G.S. et al., Crystal structure analysis of free and substrate-bound 6-hydroxy-L-nicotine oxidase from Arthrobacter nicotinovorans. J.Mol.Biol. (2010)

Release Date

2011-03-23

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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