SMTL ID : 1ng3.1

Complex of ThiO (glycine oxidase) with acetyl-glycine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-tetramer

Ligands

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

PO4.1: 4 residues within 4Å: Chain A: R.110, R.275 Chain B: R.110, R.275 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Water bridges: A:S.273 Salt bridges: A:R.110, A:R.275, B:R.110, B:R.275 PO4.6: 4 residues within 4Å: Chain C: R.110, R.275 Chain D: R.110, R.275 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain D Water bridges: C:S.273 Salt bridges: C:R.110, C:R.275, D:R.110, D:R.275

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

FAD.2: 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: AAC.3 33 PLIP interactions: 33 interactions with chain A Hydrophobic interactions: A:R.323 Hydrogen bonds: A:G.33, A:G.33, A:G.34, 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:F.349, A:G.352, A:I.353, A:L.354 Water bridges: A:G.37, A:E.55, A:S.56, A:S.56, A:G.61, A:R.62, A:T.63, A:T.64, A:G.72, A:G.224, A:G.224, A:V.225 FAD.4: 38 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.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, P.324, H.348, F.349, R.350, N.351, G.352, I.353, L.354 Ligands: AAC.5 30 PLIP interactions: 30 interactions with chain B Hydrophobic interactions: B:R.323 Hydrogen bonds: B:G.33, B:I.35, B:I.36, B:S.56, B:R.62, B:T.63, B:T.63, B:T.64, B:A.68, B:G.69, B:M.70, B:M.70, B:V.195, B:V.195, B:F.349, 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, B:G.224, B:N.351 FAD.7: 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: AAC.8 33 PLIP interactions: 33 interactions with chain C Hydrophobic interactions: C:R.323 Hydrogen bonds: C:G.33, C:G.33, C:G.34, 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:F.349, C:G.352, C:I.353, C:L.354 Water bridges: C:G.37, C:E.55, C:S.56, C:S.56, C:G.61, C:R.62, C:T.64, C:G.72, C:G.224, C:G.224, C:V.225 FAD.9: 38 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.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, P.324, H.348, F.349, R.350, N.351, G.352, I.353, L.354 Ligands: AAC.10 31 PLIP interactions: 31 interactions with chain D Hydrophobic interactions: D:R.323 Hydrogen bonds: D:G.33, D:I.35, D:I.36, 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:F.349, 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:G.224, D:V.225, D:N.351

4 x AAC: ACETYLAMINO-ACETIC ACID(Non-covalent)

AAC.3: 8 residues within 4Å: Chain A: M.70, A.75, Y.262, Y.267, A.280, R.323, R.350 Ligands: FAD.2 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:A.75 Hydrogen bonds: A:Y.267, A:R.350 Water bridges: A:G.72, A:R.350 Salt bridges: A:R.323, A:R.350 AAC.5: 9 residues within 4Å: Chain B: M.70, E.76, Y.262, Y.267, A.280, R.323, R.350, N.351 Ligands: FAD.4 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:E.76 Hydrogen bonds: B:R.350, B:R.350, B:R.350 Water bridges: B:R.350 Salt bridges: B:R.323, B:R.350 AAC.8: 8 residues within 4Å: Chain C: M.70, A.75, Y.262, Y.267, A.280, R.323, R.350 Ligands: FAD.7 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:A.75 Hydrogen bonds: C:R.350 Water bridges: C:G.72, C:R.350 Salt bridges: C:R.323, C:R.350 AAC.10: 9 residues within 4Å: Chain D: M.70, E.76, Y.262, Y.267, A.280, R.323, R.350, N.351 Ligands: FAD.9 9 PLIP interactions: 9 interactions with chain D Hydrophobic interactions: D:E.76 Hydrogen bonds: D:Y.262, D:Y.267, D:R.350, D:R.350, D:R.350 Water bridges: D:R.350 Salt bridges: D:R.323, D:R.350

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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