SMTL ID : 1pow.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 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.2 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.439, A:Q.468 MG.4: 4 residues within 4Å: Chain B: D.439, N.466, Q.468 Ligands: TPP.5 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.439, B:Q.468 MG.7: 4 residues within 4Å: Chain C: D.439, N.466, Q.468 Ligands: TPP.8 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.439, C:Q.468 MG.10: 4 residues within 4Å: Chain D: D.439, N.466, Q.468 Ligands: TPP.11 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.439, D:Q.468

4 x TPP: THIAMINE DIPHOSPHATE(Non-covalent)

TPP.2: 24 residues within 4Å: Chain A: V.386, G.387, D.388, A.412, T.413, M.414, G.438, D.439, G.440, G.441, N.466, Q.468, Y.469, G.470, F.471, I.472 Chain C: I.24, P.25, E.51, S.74, P.77, H.81, Q.114 Ligands: MG.1 16 PLIP interactions: 13 interactions with chain A, 3 interactions with chain C Hydrophobic interactions: A:Y.469, C:I.24, C:P.77 Hydrogen bonds: A:D.388, A:A.412, A:M.414, A:D.439, A:G.440, A:G.441, A:N.466, A:G.470, A:F.471, C:Q.114 Water bridges: A:G.438, A:G.438, A:G.438 TPP.5: 25 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.4 15 PLIP interactions: 13 interactions with chain B, 2 interactions with chain D Hydrophobic interactions: B:Y.469, D:I.24 Hydrogen bonds: B:D.388, B:A.412, B:M.414, B:G.440, B:G.441, B:N.466, B:G.470, B:F.471, D:Q.114 Water bridges: B:I.389, B:G.438, B:G.438, B:G.438 TPP.8: 24 residues within 4Å: Chain A: I.24, P.25, E.51, S.74, P.77, H.81, Q.114 Chain C: V.386, G.387, D.388, A.412, T.413, M.414, G.438, D.439, G.440, G.441, N.466, Q.468, Y.469, G.470, F.471, I.472 Ligands: MG.7 15 PLIP interactions: 12 interactions with chain C, 3 interactions with chain A Hydrophobic interactions: C:Y.469, A:I.24, A:P.77 Hydrogen bonds: C:D.388, C:A.412, C:M.414, C:G.440, C:G.441, C:N.466, C:G.470, C:F.471, A:Q.114 Water bridges: C:G.438, C:G.438, C:G.438 TPP.11: 25 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.10 15 PLIP interactions: 13 interactions with chain D, 2 interactions with chain B Hydrophobic interactions: D:Y.469, B:I.24 Hydrogen bonds: D:D.388, D:A.412, D:M.414, D:G.440, D:G.441, D:N.466, D:G.470, D:F.471, B:Q.114 Water bridges: D:I.389, D:G.438, D:G.438, D:G.438

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

FAD.3: 30 residues within 4Å: Chain A: 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, N.390, S.408, N.409, L.410, A.412 Chain C: F.113 24 PLIP interactions: 22 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:V.257, 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.277, 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:N.278 Salt bridges: A:H.93 FAD.6: 31 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, L.410, A.412 Chain D: F.113 21 PLIP interactions: 19 interactions with chain B, 2 interactions with chain D Hydrophobic interactions: B:V.257, B:V.386, 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:D.317, B:A.318, B:N.409 Salt bridges: B:H.93 FAD.9: 30 residues within 4Å: Chain A: F.113 Chain C: 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, N.390, S.408, N.409, L.410, A.412 26 PLIP interactions: 24 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:V.257, 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.277, 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 Salt bridges: C:H.93 FAD.12: 31 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, L.410, A.412 21 PLIP interactions: 19 interactions with chain D, 2 interactions with chain B Hydrophobic interactions: D:V.257, D:V.386, 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:D.317, D:D.317, D:A.318, D:N.409 Salt bridges: D:H.93

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