SMTL ID : 3lpl.1

E. coli pyruvate dehydrogenase complex E1 component E571A mutant

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

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

EPE.1: 7 residues within 4Å: Chain A: V.65, E.66, E.67, Q.68, P.69, E.70, K.367 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.67, A:Q.68 Water bridges: A:Y.71 Salt bridges: A:E.70, A:K.367 EPE.7: 6 residues within 4Å: Chain B: V.65, E.66, E.67, Q.68, E.70, K.367 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:E.66, B:Q.68 Water bridges: B:S.296, B:D.299, B:K.367 Salt bridges: B:K.367

2 x TPP: THIAMINE DIPHOSPHATE(Non-covalent)

TPP.2: 13 residues within 4Å: Chain A: S.109, Q.140, G.229, D.230, G.231, E.232, N.258, N.260, Q.262, R.263, L.264 Chain B: I.569 Ligands: MG.3 13 PLIP interactions: 12 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:L.264, B:I.569 Hydrogen bonds: A:Q.140, A:Q.140, A:D.230, A:G.231, A:E.232, A:N.258, A:N.260, A:R.263 Water bridges: A:G.229, A:G.229 Salt bridges: A:K.392 TPP.5: 16 residues within 4Å: Chain A: I.569 Chain B: S.109, Q.140, H.142, 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 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:L.264 Hydrogen bonds: B:Q.140, B:D.230, B:G.231, B:E.232, B:N.258, B:N.260 Water bridges: B:G.229, B:E.232, B:N.260 Salt bridges: B:H.142, B:H.142, B:K.392, B:K.392

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 6 residues within 4Å: Chain A: G.229, D.230, N.258, N.260, Q.262 Ligands: TPP.2 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.230, A:N.258 MG.6: 4 residues within 4Å: Chain B: D.230, 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.24

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

PO4.4: 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:R.86 Salt bridges: A:R.79, A:R.82, A:R.86 PO4.8: 6 residues within 4Å: Chain B: R.79, R.82, R.86, T.115, Y.394, F.424 5 PLIP interactions: 5 interactions with chain B Water bridges: B:R.86, B:R.86 Salt bridges: B:R.79, B:R.82, B:R.86

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