SMTL ID : 1pj6.1 (1 other biounit)

Crystal structure of dimethylglycine oxidase of Arthrobacter globiformis in complex with folic acid

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

homo-tetramer

Ligands

4 x NA: SODIUM ION(Non-functional Binders)

NA.1: 2 residues within 4Å: Chain A: D.257, V.412 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.257 NA.4: 2 residues within 4Å: Chain B: D.257, V.412 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:V.412 NA.7: 2 residues within 4Å: Chain C: D.257, V.412 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:V.412 NA.10: 2 residues within 4Å: Chain D: D.257, V.412 No protein-ligand interaction detected (PLIP)

4 x FOL: FOLIC ACID(Non-covalent)

FOL.2: 11 residues within 4Å: Chain A: L.508, Y.539, T.554, Y.631, F.632, L.649, S.650, Y.651, E.658, Y.699, F.719 23 PLIP interactions: 23 interactions with chain A Hydrophobic interactions: A:Y.539, A:Y.539, A:F.632, A:F.632, A:Y.699, A:F.719 Hydrogen bonds: A:Y.631 Water bridges: A:K.532, A:K.532, A:V.537, A:V.537, A:Y.539, A:D.552, A:D.552, A:T.554, A:T.554, A:T.554, A:F.632, A:Y.651, A:E.658 Salt bridges: A:E.658 pi-Stacking: A:Y.651, A:Y.651 FOL.5: 11 residues within 4Å: Chain B: L.508, Y.539, T.554, Y.631, F.632, L.649, S.650, Y.651, E.658, Y.699, F.719 23 PLIP interactions: 23 interactions with chain B Hydrophobic interactions: B:Y.539, B:Y.539, B:F.632, B:F.632, B:Y.699, B:F.719 Hydrogen bonds: B:Y.631 Water bridges: B:K.532, B:K.532, B:V.537, B:V.537, B:Y.539, B:D.552, B:D.552, B:T.554, B:T.554, B:T.554, B:F.632, B:Y.651, B:E.658 Salt bridges: B:E.658 pi-Stacking: B:Y.651, B:Y.651 FOL.8: 11 residues within 4Å: Chain C: L.508, Y.539, T.554, Y.631, F.632, L.649, S.650, Y.651, E.658, Y.699, F.719 23 PLIP interactions: 23 interactions with chain C Hydrophobic interactions: C:Y.539, C:Y.539, C:F.632, C:F.632, C:Y.699, C:F.719 Water bridges: C:K.532, C:K.532, C:V.537, C:V.537, C:Y.539, C:Y.539, C:Y.539, C:T.554, C:T.554, C:F.632, C:Y.651, C:E.658, C:E.658, C:Y.660 Salt bridges: C:E.658 pi-Stacking: C:Y.651, C:Y.651 FOL.11: 11 residues within 4Å: Chain D: L.508, Y.539, T.554, Y.631, F.632, L.649, S.650, Y.651, E.658, Y.699, F.719 23 PLIP interactions: 23 interactions with chain D Hydrophobic interactions: D:Y.539, D:Y.539, D:F.632, D:F.632, D:Y.699, D:F.719 Water bridges: D:K.532, D:K.532, D:V.537, D:V.537, D:Y.539, D:Y.539, D:Y.539, D:T.554, D:T.554, D:F.632, D:Y.651, D:E.658, D:E.658, D:Y.660 Salt bridges: D:E.658 pi-Stacking: D:Y.651, D:Y.651

4 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Covalent)

FAD.3: 31 residues within 4Å: Chain A: G.11, G.13, I.14, V.15, D.35, Q.36, P.42, G.44, S.45, T.46, H.48, A.49, P.50, G.51, L.52, T.172, T.173, V.174, C.202, A.203, G.204, W.206, I.210, H.225, Y.259, G.333, I.334, V.360, W.361, V.362, T.363 26 PLIP interactions: 26 interactions with chain A Hydrophobic interactions: A:P.50 Hydrogen bonds: A:V.15, A:Q.36, A:G.44, A:S.45, A:T.46, A:T.46, A:G.51, A:L.52, A:L.52, A:V.174, A:V.174, A:G.204, A:Y.259, A:V.362, A:T.363 Water bridges: A:G.13, A:G.13, A:Q.36, A:Q.36, A:G.43, A:G.43, A:F.205, A:F.205, A:V.360 pi-Stacking: A:W.206 FAD.6: 31 residues within 4Å: Chain B: G.11, G.13, I.14, V.15, D.35, Q.36, P.42, G.44, S.45, T.46, H.48, A.49, P.50, G.51, L.52, T.172, T.173, V.174, C.202, A.203, G.204, W.206, I.210, H.225, Y.259, G.333, I.334, V.360, W.361, V.362, T.363 26 PLIP interactions: 26 interactions with chain B Hydrophobic interactions: B:P.50 Hydrogen bonds: B:V.15, B:Q.36, B:G.44, B:S.45, B:T.46, B:T.46, B:G.51, B:L.52, B:L.52, B:V.174, B:V.174, B:G.204, B:Y.259, B:V.362, B:T.363 Water bridges: B:G.13, B:G.13, B:Q.36, B:Q.36, B:G.43, B:G.43, B:F.205, B:F.205, B:V.360 pi-Stacking: B:W.206 FAD.9: 31 residues within 4Å: Chain C: G.11, G.13, I.14, V.15, D.35, Q.36, P.42, G.44, S.45, T.46, H.48, A.49, P.50, G.51, L.52, T.172, T.173, V.174, C.202, A.203, G.204, W.206, I.210, H.225, Y.259, G.333, I.334, V.360, W.361, V.362, T.363 26 PLIP interactions: 26 interactions with chain C Hydrophobic interactions: C:P.50 Hydrogen bonds: C:V.15, C:Q.36, C:G.44, C:S.45, C:T.46, C:T.46, C:G.51, C:L.52, C:L.52, C:V.174, C:V.174, C:G.204, C:V.362, C:T.363, C:T.363 Water bridges: C:G.13, C:G.13, C:Q.36, C:Q.36, C:G.43, C:G.43, C:F.205, C:F.205, C:V.360 pi-Stacking: C:W.206 FAD.12: 31 residues within 4Å: Chain D: G.11, G.13, I.14, V.15, D.35, Q.36, P.42, G.44, S.45, T.46, H.48, A.49, P.50, G.51, L.52, T.172, T.173, V.174, C.202, A.203, G.204, W.206, I.210, H.225, Y.259, G.333, I.334, V.360, W.361, V.362, T.363 26 PLIP interactions: 26 interactions with chain D Hydrophobic interactions: D:P.50 Hydrogen bonds: D:V.15, D:Q.36, D:G.44, D:S.45, D:T.46, D:T.46, D:G.51, D:L.52, D:L.52, D:V.174, D:V.174, D:G.204, D:V.362, D:T.363, D:T.363 Water bridges: D:G.13, D:G.13, D:Q.36, D:Q.36, D:G.43, D:G.43, D:F.205, D:F.205, D:V.360 pi-Stacking: D:W.206

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Leys, D. et al., Channelling and formation of 'active' formaldehyde in dimethylglycine oxidase. Embo J. (2003)

Release Date

2003-10-07

Peptides

N,N-dimethylglycine oxidase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

N,N-dimethylglycine oxidase

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