SMTL ID : 1zpd.1

PYRUVATE DECARBOXYLASE FROM ZYMOMONAS MOBILIS

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.86 Å

Oligo State

homo-tetramer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: D.440, G.441, N.467, G.469 Ligands: DPX.2 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.440, A:G.469, H2O.1 MG.4: 4 residues within 4Å: Chain B: D.440, N.467, G.469 Ligands: DPX.5 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.440, B:G.469, H2O.25 MG.7: 5 residues within 4Å: Chain C: D.440, G.441, N.467, G.469 Ligands: DPX.8 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.440, C:G.469, H2O.50 MG.10: 4 residues within 4Å: Chain D: D.440, N.467, G.469 Ligands: DPX.11 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.440, D:G.469, H2O.75

4 x DPX: MONO-{4-[(4-AMINO-2-METHYL-PYRIMIDIN-5-YLMETHYL)-AMINO]-2-HYDROXY-3-MERCAPTO-PENT-3-ENYL-PHOSPHONO} ESTER(Non-covalent)

DPX.2: 23 residues within 4Å: Chain A: T.388, G.389, D.390, G.413, H.414, I.415, G.439, D.440, G.441, S.442, L.445, N.467, G.469, Y.470, T.471, I.472, E.473 Chain B: A.25, G.26, E.50, V.75, H.114 Ligands: MG.1 24 PLIP interactions: 23 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:I.415, A:I.415, A:L.445, A:Y.470 Hydrogen bonds: A:D.390, A:G.413, A:I.415, A:G.439, A:G.441, A:S.442, A:N.467, A:G.469, A:T.471, A:T.471, A:I.472, A:E.473 Water bridges: A:D.390, A:S.391, A:D.440, A:D.440, A:S.442, A:S.442, A:E.473, B:D.27 DPX.5: 23 residues within 4Å: Chain A: A.25, G.26, E.50, V.75, H.114 Chain B: T.388, G.389, D.390, G.413, H.414, I.415, G.439, D.440, G.441, S.442, L.445, N.467, G.469, Y.470, T.471, I.472, E.473 Ligands: MG.4 23 PLIP interactions: 22 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:I.415, B:I.415, B:L.445, B:Y.470 Hydrogen bonds: B:D.390, B:G.413, B:I.415, B:G.439, B:G.441, B:S.442, B:N.467, B:G.469, B:T.471, B:T.471, B:I.472, B:E.473 Water bridges: B:S.391, B:D.440, B:D.440, B:S.442, B:S.442, B:E.473, A:D.27 DPX.8: 23 residues within 4Å: Chain C: T.388, G.389, D.390, G.413, H.414, I.415, G.439, D.440, G.441, S.442, L.445, N.467, G.469, Y.470, T.471, I.472, E.473 Chain D: A.25, G.26, E.50, V.75, H.114 Ligands: MG.7 22 PLIP interactions: 20 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:I.415, C:I.415, C:L.445, C:Y.470 Hydrogen bonds: C:D.390, C:G.413, C:I.415, C:G.439, C:G.441, C:S.442, C:N.467, C:G.469, C:T.471, C:I.472, C:E.473 Water bridges: C:S.391, C:D.440, C:D.440, C:S.442, C:E.473, D:D.27, D:E.50 DPX.11: 23 residues within 4Å: Chain C: A.25, G.26, E.50, V.75, H.114 Chain D: T.388, G.389, D.390, G.413, H.414, I.415, G.439, D.440, G.441, S.442, L.445, N.467, G.469, Y.470, T.471, I.472, E.473 Ligands: MG.10 24 PLIP interactions: 21 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: D:I.415, D:I.415, D:L.445, D:Y.470, C:V.75 Hydrogen bonds: D:D.390, D:G.413, D:I.415, D:G.439, D:G.441, D:S.442, D:N.467, D:G.469, D:T.471, D:I.472, D:E.473 Water bridges: D:S.391, D:D.440, D:D.440, D:S.442, D:S.442, D:E.473, C:D.27, C:E.50

4 x CIT: CITRIC ACID(Non-functional Binders)

CIT.3: 8 residues within 4Å: Chain A: R.310, S.311, R.318, P.320, S.321 Chain D: H.150, K.153, R.157 17 PLIP interactions: 10 interactions with chain A, 7 interactions with chain D Hydrophobic interactions: A:R.310 Hydrogen bonds: A:S.311, A:S.321, D:K.153 Water bridges: A:R.310, A:R.310, A:R.310, A:S.311, A:R.318, D:R.157, D:R.157 Salt bridges: A:R.310, A:R.318, D:H.150, D:K.153, D:K.153, D:R.157 CIT.6: 9 residues within 4Å: Chain B: E.188, R.310, S.311, R.318, P.320, S.321 Chain C: H.150, K.153, R.157 16 PLIP interactions: 9 interactions with chain B, 7 interactions with chain C Hydrophobic interactions: B:R.310 Hydrogen bonds: B:S.311, B:S.321, C:K.153 Water bridges: B:R.310, B:R.310, B:S.311, B:R.318, C:R.157, C:R.157 Salt bridges: B:R.310, B:R.318, C:H.150, C:K.153, C:K.153, C:R.157 CIT.9: 8 residues within 4Å: Chain B: H.150, K.153, R.157 Chain C: R.310, S.311, R.318, P.320, S.321 17 PLIP interactions: 10 interactions with chain C, 7 interactions with chain B Hydrophobic interactions: C:R.310 Hydrogen bonds: C:S.311, C:S.321, B:K.153 Water bridges: C:R.310, C:R.310, C:R.310, C:S.311, C:R.318, B:R.157, B:R.157 Salt bridges: C:R.310, C:R.318, B:H.150, B:K.153, B:K.153, B:R.157 CIT.12: 8 residues within 4Å: Chain A: H.150, K.153, R.157 Chain D: R.310, S.311, R.318, P.320, S.321 17 PLIP interactions: 10 interactions with chain D, 7 interactions with chain A Hydrophobic interactions: D:R.310 Hydrogen bonds: D:S.311, D:S.321, A:K.153 Water bridges: D:R.310, D:R.310, D:R.310, D:S.311, D:R.318, A:R.157, A:R.157 Salt bridges: D:R.310, D:R.318, A:H.150, A:K.153, A:K.153, A:R.157

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dobritzsch, D. et al., High resolution crystal structure of pyruvate decarboxylase from Zymomonas mobilis. Implications for substrate activation in pyruvate decarboxylases. J.Biol.Chem. (1998)

Release Date

1999-02-02

Peptides

PYRUVATE DECARBOXYLASE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
E

D
F

PYRUVATE DECARBOXYLASE