SMTL ID : 3k7q.1

Crystal structure of substrate-bound 6-hydroxy-L-nicotine oxidase from Arthrobacter nicotinovorans

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.05 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.4: 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.5 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: 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: HNL.1 38 PLIP interactions: 38 interactions with chain A Hydrophobic interactions: A:R.39, A:K.287, A:P.370, A:W.371, A:W.371 Hydrogen bonds: A:G.9, A:G.10, A:S.12, A:G.32, A:G.33, 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:T.259, A:D.399, A:E.409 Salt bridges: A:R.39, A:R.39 pi-Stacking: A:W.371 FAD.5: 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: HNL.4 36 PLIP interactions: 36 interactions with chain B Hydrophobic interactions: B:R.39, B:K.287, B:P.370, B:W.371, B:W.371 Hydrogen bonds: B:G.9, B:G.10, B:S.12, B:G.32, B:G.33, 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: 22 residues within 4Å: Chain A: A.100, F.101, T.115, L.152, S.156, F.159, L.160, W.163, M.180, I.191, L.192, V.194, V.195, L.196 Chain B: V.97, F.101, I.103, P.104, G.105, A.108, E.112 Ligands: GP7.6 17 PLIP interactions: 11 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:F.101, A:L.152, A:F.159, A:L.160, A:L.160, A:W.163, A:I.191, A:L.192, A:V.195, A:L.196, B:F.101, B:A.108, B:E.112 Water bridges: A:A.100, B:S.106, B:S.106 Hydrogen bonds: B:G.105 GP7.6: 22 residues within 4Å: Chain A: V.97, F.101, I.103, P.104, G.105, A.108, E.112 Chain B: A.100, F.101, T.115, L.152, S.156, F.159, L.160, W.163, M.180, I.191, L.192, V.194, V.195, L.196 Ligands: GP7.3 17 PLIP interactions: 11 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:F.101, B:L.152, B:F.159, B:L.160, B:L.160, B:W.163, B:I.191, B:L.192, B:V.195, B:L.196, A:F.101, A:A.108, A:E.112 Water bridges: B:A.100, A:S.106, A:S.106 Hydrogen bonds: A:G.105

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

2010-01-19

Peptides

6-hydroxy-L-nicotine oxidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
X

B
X

6-hydroxy-L-nicotine oxidase

Related Entries With Identical Sequence