SMTL ID : 3lq4.1

E. coli pyruvate dehydrogenase complex E1 E235A mutant with high TDP concentration

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.98 Å

Oligo State

homo-dimer

Ligands

2 x TPP: THIAMINE DIPHOSPHATE(Non-covalent)

TPP.1: 23 residues within 4Å: Chain A: S.109, Q.140, H.142, V.192, M.194, G.229, D.230, G.231, E.232, N.258, N.260, Q.262, R.263, L.264, K.392 Chain B: D.521, E.522, I.569, E.571, F.602, R.606, H.640 Ligands: MG.2 18 PLIP interactions: 14 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:L.264, B:I.569, B:I.569, B:F.602 Hydrogen bonds: A:Q.140, A:Q.140, A:V.192, A:M.194, A:G.231, A:E.232, A:N.258, A:R.263 Water bridges: A:G.229, A:D.230, A:D.230, A:E.232 Salt bridges: A:K.392 pi-Stacking: B:F.602 TPP.5: 22 residues within 4Å: Chain A: D.521, I.569, E.571, F.602, H.640 Chain B: S.109, Q.140, H.142, V.192, S.193, M.194, G.229, D.230, G.231, E.232, N.258, N.260, Q.262, R.263, L.264, K.392 Ligands: MG.6 21 PLIP interactions: 17 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:M.194, B:L.264, A:I.569, A:I.569, A:F.602 Hydrogen bonds: B:Q.140, B:Q.140, B:V.192, B:M.194, B:D.230, B:G.231, B:E.232, B:N.258, B:N.260, B:R.263 Water bridges: B:G.229, B:G.229 Salt bridges: B:H.142, B:K.392, B:K.392 pi-Stacking: A:F.602

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: D.230, N.258, N.260, Q.262 Ligands: TPP.1 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.230, A:Q.262, H2O.1 MG.6: 5 residues within 4Å: Chain B: D.230, N.258, N.260, Q.262 Ligands: TPP.5 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.230, B:Q.262, H2O.20

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

PO4.3: 5 residues within 4Å: Chain A: R.79, R.82, R.86, Y.394, F.424 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Y.394, A:R.423 Water bridges: A:R.86, A:H.364 Salt bridges: A:R.79, A:R.82, A:R.86 PO4.7: 6 residues within 4Å: Chain B: R.79, R.82, R.86, T.115, Y.394, F.424 3 PLIP interactions: 3 interactions with chain B Salt bridges: B:R.79, B:R.82, B:R.86

1 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.4: 7 residues within 4Å: Chain A: V.65, E.66, E.67, Q.68, P.69, E.70, K.367 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.67, A:Q.68 Water bridges: A:E.70, A:Y.71 Salt bridges: A:E.70, A:K.367

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nemeria, N.S. et al., Communication between thiamin cofactors in the Escherichia coli pyruvate dehydrogenase complex E1 component active centers: evidence for a "direct pathway" between the 4'-aminopyrimidine N1' atoms. J.Biol.Chem. (2010)

Release Date

2010-03-02

Peptides

Pyruvate dehydrogenase E1 component: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Pyruvate dehydrogenase E1 component

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