SMTL ID : 1ng4.1

Structure of ThiO (glycine oxidase) from Bacillus subtilis

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-tetramer

Ligands

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

FAD.1: 37 residues within 4Å: Chain A: I.31, G.32, G.33, G.34, I.35, I.36, F.54, E.55, S.56, R.62, T.63, T.64, A.66, A.67, A.68, G.69, M.70, P.194, V.195, A.222, S.223, G.224, W.226, F.230, G.245, C.247, Y.267, G.321, R.323, H.348, F.349, R.350, N.351, G.352, I.353, L.354 Ligands: PEO.2 28 PLIP interactions: 28 interactions with chain A Hydrophobic interactions: A:R.323 Hydrogen bonds: A:G.33, A:I.36, A:S.56, A:R.62, A:T.63, A:T.63, A:T.64, A:T.64, A:A.68, A:G.69, A:M.70, A:M.70, A:V.195, A:V.195, A:G.224, A:H.348, A:G.352, A:I.353, A:L.354 Water bridges: A:G.34, A:E.55, A:G.61, A:R.62, A:T.63, A:T.64, A:G.72, A:V.225 FAD.4: 36 residues within 4Å: Chain B: I.31, G.32, G.33, G.34, I.35, I.36, F.54, E.55, S.56, R.62, T.63, T.64, A.67, A.68, G.69, M.70, P.194, V.195, A.222, S.223, G.224, W.226, F.230, G.245, C.247, Y.267, G.321, R.323, H.348, F.349, R.350, N.351, G.352, I.353, L.354 Ligands: PEO.5 30 PLIP interactions: 30 interactions with chain B Hydrophobic interactions: B:R.323 Hydrogen bonds: B:G.33, B:I.36, B:S.56, B:S.56, B:R.62, B:T.63, B:T.63, B:T.64, B:T.64, B:A.68, B:G.69, B:M.70, B:M.70, B:V.195, B:V.195, B:G.224, B:H.348, B:G.352, B:I.353, B:L.354 Water bridges: B:G.34, B:G.34, B:E.55, B:G.61, B:R.62, B:T.63, B:T.63, B:T.64, B:G.72 FAD.6: 37 residues within 4Å: Chain C: I.31, G.32, G.33, G.34, I.35, I.36, F.54, E.55, S.56, R.62, T.63, T.64, A.66, A.67, A.68, G.69, M.70, P.194, V.195, A.222, S.223, G.224, W.226, F.230, G.245, C.247, Y.267, G.321, R.323, H.348, F.349, R.350, N.351, G.352, I.353, L.354 Ligands: PEO.7 28 PLIP interactions: 28 interactions with chain C Hydrophobic interactions: C:R.323 Hydrogen bonds: C:G.33, C:I.36, C:S.56, C:R.62, C:T.63, C:T.63, C:T.63, C:T.64, C:T.64, C:A.68, C:G.69, C:M.70, C:M.70, C:V.195, C:V.195, C:G.224, C:H.348, C:G.352, C:I.353, C:L.354 Water bridges: C:G.34, C:E.55, C:G.61, C:R.62, C:T.64, C:G.72, C:V.225 FAD.9: 36 residues within 4Å: Chain D: I.31, G.32, G.33, G.34, I.35, I.36, F.54, E.55, S.56, R.62, T.63, T.64, A.67, A.68, G.69, M.70, P.194, V.195, A.222, S.223, G.224, W.226, F.230, G.245, C.247, Y.267, G.321, R.323, H.348, F.349, R.350, N.351, G.352, I.353, L.354 Ligands: PEO.10 30 PLIP interactions: 30 interactions with chain D Hydrophobic interactions: D:R.323 Hydrogen bonds: D:G.33, D:I.36, D:S.56, D:S.56, D:R.62, D:T.63, D:T.63, D:T.63, D:T.64, D:T.64, D:A.68, D:G.69, D:M.70, D:M.70, D:V.195, D:V.195, D:G.224, D:H.348, D:G.352, D:I.353, D:L.354 Water bridges: D:G.34, D:G.34, D:E.55, D:G.61, D:R.62, D:T.64, D:G.72, D:V.225

4 x PEO: HYDROGEN PEROXIDE(Non-functional Binders)

PEO.2: 5 residues within 4Å: Chain A: Y.267, A.280, R.323, R.350 Ligands: FAD.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.323, A:R.350 Water bridges: A:R.350, A:R.350 PEO.5: 3 residues within 4Å: Chain B: R.323, R.350 Ligands: FAD.4 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.323, B:R.323 PEO.7: 5 residues within 4Å: Chain C: Y.267, A.280, R.323, R.350 Ligands: FAD.6 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:R.323, C:R.323, C:R.350 Water bridges: C:H.265, C:R.350, C:R.350 PEO.10: 3 residues within 4Å: Chain D: R.323, R.350 Ligands: FAD.9 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:R.323 Water bridges: D:H.265, D:R.350

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.3: 4 residues within 4Å: Chain A: R.110, R.275 Chain B: R.110, R.275 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Water bridges: A:S.273, B:S.273 Salt bridges: A:R.110, A:R.275, B:R.110, B:R.275 PO4.8: 4 residues within 4Å: Chain C: R.110, R.275 Chain D: R.110, R.275 6 PLIP interactions: 3 interactions with chain C, 3 interactions with chain D Water bridges: C:S.273, D:S.273 Salt bridges: C:R.110, C:R.275, D:R.110, D:R.275

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Settembre, E.C. et al., Structural and Mechanistic Studies on ThiO, a Glycine Oxidase Essential for Thiamin Biosynthesis in Bacillus subtilis. Biochemistry (2003)

Release Date

2003-04-08

Peptides

Glycine oxidase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Glycine oxidase

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