SMTL ID : 1pox.1

THE REFINED STRUCTURES OF A STABILIZED MUTANT AND OF WILD-TYPE PYRUVATE OXIDASE FROM LACTOBACILLUS PLANTARUM

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-tetramer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: D.439, N.466, Q.468 Ligands: TPP.5 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.439, A:Q.468, H2O.165 MG.3: 4 residues within 4Å: Chain B: D.439, N.466, Q.468 Ligands: TPP.7 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.439, B:Q.468, H2O.428 MG.11: 4 residues within 4Å: Chain C: D.439, N.466, Q.468 Ligands: TPP.15 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.439, C:Q.468, H2O.904 MG.13: 4 residues within 4Å: Chain D: D.439, N.466, Q.468 Ligands: TPP.17 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.439, D:Q.468, H2O.1167

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

NA.2: 5 residues within 4Å: Chain A: M.444, Q.447 Chain C: M.444, Q.447 Ligands: NA.12 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:M.444, A:Q.447 Water bridges: C:Q.447 NA.4: 5 residues within 4Å: Chain B: M.444, Q.447 Chain D: M.444, Q.447 Ligands: NA.14 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:Q.447, B:Q.447, D:Q.447 NA.12: 5 residues within 4Å: Chain A: M.444, Q.447 Chain C: M.444, Q.447 Ligands: NA.2 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:M.444, A:Q.447 Water bridges: C:Q.447 NA.14: 5 residues within 4Å: Chain B: M.444, Q.447 Chain D: M.444, Q.447 Ligands: NA.4 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain D Hydrogen bonds: B:Q.447, D:Q.447, D:Q.447

4 x TPP: THIAMINE DIPHOSPHATE(Non-covalent)

TPP.5: 26 residues within 4Å: Chain A: V.386, G.387, D.388, A.412, M.414, G.438, D.439, G.440, G.441, M.444, N.466, Q.468, Y.469, G.470, F.471, I.472 Chain C: I.24, P.25, E.51, S.74, P.77, G.78, H.81, Q.114 Ligands: MG.1, GOL.9 19 PLIP interactions: 17 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:Y.469, C:I.24 Hydrogen bonds: A:D.388, A:A.412, A:M.414, A:D.439, A:G.440, A:G.441, A:N.466, A:Q.468, A:G.470, A:F.471, C:Q.114 Water bridges: A:I.389, A:G.438, A:G.438, A:G.438, A:D.439, A:D.439 TPP.7: 26 residues within 4Å: Chain B: V.386, G.387, D.388, A.412, M.414, G.438, D.439, G.440, G.441, M.444, N.466, Q.468, Y.469, G.470, F.471, I.472 Chain D: I.24, P.25, E.51, S.74, P.77, G.78, H.81, Q.114 Ligands: MG.3, GOL.10 20 PLIP interactions: 4 interactions with chain D, 16 interactions with chain B Hydrophobic interactions: D:I.24, D:P.77, B:Y.469 Hydrogen bonds: D:S.74, D:Q.114, B:D.388, B:A.412, B:M.414, B:D.439, B:G.440, B:G.441, B:N.466, B:Q.468, B:G.470, B:F.471 Water bridges: B:I.389, B:G.438, B:G.438, B:D.439, B:D.439 TPP.15: 26 residues within 4Å: Chain A: I.24, P.25, E.51, S.74, P.77, G.78, H.81, Q.114 Chain C: V.386, G.387, D.388, A.412, M.414, G.438, D.439, G.440, G.441, M.444, N.466, Q.468, Y.469, G.470, F.471, I.472 Ligands: MG.11, GOL.19 20 PLIP interactions: 17 interactions with chain C, 3 interactions with chain A Hydrophobic interactions: C:Y.469, A:I.24 Hydrogen bonds: C:D.388, C:D.388, C:A.412, C:M.414, C:G.440, C:G.441, C:N.466, C:Q.468, C:G.470, C:F.471, A:Q.114 Water bridges: C:I.389, C:G.438, C:G.438, C:G.438, C:D.439, C:D.439, A:E.51 TPP.17: 26 residues within 4Å: Chain B: I.24, P.25, E.51, S.74, P.77, G.78, H.81, Q.114 Chain D: V.386, G.387, D.388, A.412, M.414, G.438, D.439, G.440, G.441, M.444, N.466, Q.468, Y.469, G.470, F.471, I.472 Ligands: MG.13, GOL.20 20 PLIP interactions: 16 interactions with chain D, 4 interactions with chain B Hydrophobic interactions: D:Y.469, B:I.24, B:P.77 Hydrogen bonds: D:D.388, D:D.388, D:A.412, D:M.414, D:G.440, D:G.441, D:N.466, D:Q.468, D:G.470, D:F.471, B:S.74, B:Q.114 Water bridges: D:I.389, D:G.438, D:G.438, D:D.439, D:D.439

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

FAD.6: 31 residues within 4Å: Chain A: H.93, G.212, I.213, G.214, T.236, Y.237, P.238, S.253, A.254, N.255, R.256, V.257, G.276, N.277, N.278, Y.279, P.280, F.281, D.298, I.299, D.300, K.303, A.316, D.317, A.318, V.386, N.390, S.408, N.409, A.412 Chain C: F.113 25 PLIP interactions: 23 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:V.257, A:V.386, A:A.412, C:F.113, C:F.113 Hydrogen bonds: A:I.213, A:G.214, A:T.236, A:Y.237, A:A.254, A:R.256, A:V.257, A:N.278, A:I.299, A:K.303, A:K.303, A:D.317, A:A.318, A:N.409 Water bridges: A:A.254, A:N.278, A:N.278, A:Q.319, A:N.409 Salt bridges: A:H.93 FAD.8: 30 residues within 4Å: Chain B: H.93, G.212, I.213, G.214, T.236, Y.237, P.238, A.254, N.255, R.256, V.257, G.276, N.277, N.278, Y.279, P.280, F.281, D.298, I.299, D.300, K.303, A.316, D.317, A.318, V.386, N.390, S.408, N.409, A.412 Chain D: F.113 27 PLIP interactions: 25 interactions with chain B, 2 interactions with chain D Hydrophobic interactions: B:V.257, B:V.386, B:A.412, D:F.113, D:F.113 Hydrogen bonds: B:I.213, B:G.214, B:T.236, B:T.236, B:Y.237, B:A.254, B:R.256, B:V.257, B:N.277, B:N.278, B:I.299, B:K.303, B:K.303, B:D.317, B:A.318, B:N.409 Water bridges: B:N.278, B:N.278, B:N.278, B:Q.319, B:N.409 Salt bridges: B:H.93 FAD.16: 31 residues within 4Å: Chain A: F.113 Chain C: H.93, G.212, I.213, G.214, T.236, Y.237, P.238, S.253, A.254, N.255, R.256, V.257, G.276, N.277, N.278, Y.279, P.280, F.281, D.298, I.299, D.300, K.303, A.316, D.317, A.318, V.386, N.390, S.408, N.409, A.412 28 PLIP interactions: 26 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:V.257, C:V.386, C:A.412, A:F.113, A:F.113 Hydrogen bonds: C:I.213, C:G.214, C:T.236, C:T.236, C:Y.237, C:A.254, C:R.256, C:V.257, C:N.278, C:I.299, C:K.303, C:K.303, C:D.317, C:D.317, C:A.318, C:N.409 Water bridges: C:A.254, C:N.278, C:N.278, C:N.278, C:Q.319, C:N.409 Salt bridges: C:H.93 FAD.18: 30 residues within 4Å: Chain B: F.113 Chain D: H.93, G.212, I.213, G.214, T.236, Y.237, P.238, A.254, N.255, R.256, V.257, G.276, N.277, N.278, Y.279, P.280, F.281, D.298, I.299, D.300, K.303, A.316, D.317, A.318, V.386, N.390, S.408, N.409, A.412 27 PLIP interactions: 25 interactions with chain D, 2 interactions with chain B Hydrophobic interactions: D:V.257, D:V.386, D:A.412, B:F.113, B:F.113 Hydrogen bonds: D:I.213, D:G.214, D:T.236, D:Y.237, D:A.254, D:R.256, D:V.257, D:N.277, D:N.278, D:I.299, D:K.303, D:K.303, D:D.317, D:D.317, D:A.318, D:N.409 Water bridges: D:N.278, D:N.278, D:N.278, D:Q.319, D:N.409 Salt bridges: D:H.93

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 9 residues within 4Å: Chain A: F.471, I.472, E.475 Chain C: G.26, G.27, S.28, S.74, Q.114 Ligands: TPP.5 7 PLIP interactions: 6 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:G.27, C:S.28, C:S.28, C:S.74, A:E.475 Water bridges: C:S.74, C:Q.114 GOL.10: 9 residues within 4Å: Chain B: F.471, I.472, E.475 Chain D: G.26, G.27, S.28, S.74, Q.114 Ligands: TPP.7 7 PLIP interactions: 6 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:G.27, D:S.28, D:S.28, D:S.74, B:E.475 Water bridges: D:Q.114, D:Q.114 GOL.19: 9 residues within 4Å: Chain A: G.26, G.27, S.28, S.74, Q.114 Chain C: F.471, I.472, E.475 Ligands: TPP.15 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:G.27, A:S.28, A:S.28, A:S.74, C:E.475 Water bridges: A:S.74, A:Q.114 GOL.20: 9 residues within 4Å: Chain B: G.26, G.27, S.28, S.74, Q.114 Chain D: F.471, I.472, E.475 Ligands: TPP.17 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:G.27, B:S.28, B:S.28, B:S.74, D:E.475 Water bridges: B:Q.114, B:Q.114

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Muller, Y.A. et al., The refined structures of a stabilized mutant and of wild-type pyruvate oxidase from Lactobacillus plantarum. J.Mol.Biol. (1994)

Release Date

1994-01-31

Peptides

PYRUVATE OXIDASE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

PYRUVATE OXIDASE