SMTL ID : 2g25.1

E. Coli Pyruvate Dehydrogenase Phosphonolactylthiamin Diphosphate Complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain B: D.230, N.260, Q.262 Ligands: TDK.4 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.230, B:Q.262, H2O.11 MG.5: 4 residues within 4Å: Chain A: D.230, N.260, Q.262 Ligands: TDK.9 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.230, A:Q.262, H2O.15

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

PO4.2: 6 residues within 4Å: Chain A: R.79, R.82, R.86, T.115, Y.394, F.424 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:T.115, A:Y.394 Water bridges: A:R.86, A:R.86, A:R.86 Salt bridges: A:R.79, A:R.82, A:R.86 PO4.3: 5 residues within 4Å: Chain A: N.693, E.694, N.695, R.834 Chain B: E.102 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.695 Salt bridges: A:R.834 PO4.6: 5 residues within 4Å: Chain B: R.79, R.82, R.86, Y.394, F.424 9 PLIP interactions: 9 interactions with chain B Water bridges: B:R.79, B:R.79, B:R.86, B:R.86, B:R.86, B:R.86 Salt bridges: B:R.79, B:R.82, B:R.86 PO4.7: 2 residues within 4Å: Chain A: L.101 Chain B: R.834 6 PLIP interactions: 6 interactions with chain B Water bridges: B:E.694, B:R.834, B:R.834, B:R.834, B:R.834 Salt bridges: B:R.834 PO4.8: 5 residues within 4Å: Chain A: E.102 Chain B: N.693, E.694, N.695, R.834 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.695, B:N.695 Water bridges: B:N.693, B:N.695 Salt bridges: B:R.834

2 x TDK: 3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-2-{(1S)-1-HYDROXY-1-[(R)-HYDROXY(METHOXY)PHOSPHORYL]ETHYL}-5-(2-{[(S)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}ETHYL)-4-METHYL-1,3-THIAZOL-3-IUM(Non-covalent)

TDK.4: 30 residues within 4Å: Chain A: D.521, E.522, I.569, E.571, Y.599, F.602, R.606, E.636, H.640 Chain B: H.106, S.109, Q.140, H.142, Y.177, V.192, S.193, M.194, G.229, D.230, G.231, E.232, E.235, N.258, N.260, Q.262, R.263, L.264, K.392, H.407 Ligands: MG.1 26 PLIP interactions: 22 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:H.142, B:M.194, B:L.264, A:I.569, A:I.569, A:F.602 Hydrogen bonds: B:S.109, B:Q.140, B:Y.177, B:V.192, B:M.194, B:G.229, B:D.230, B:G.231, B:E.232, B:E.235, B:N.258, B:N.260, A:E.522 Water bridges: B:G.229, B:E.232 Salt bridges: B:H.142, B:K.392, B:K.392, B:H.407 pi-Stacking: B:H.142 TDK.9: 30 residues within 4Å: Chain A: H.106, S.109, Q.140, H.142, Y.177, V.192, S.193, M.194, G.229, D.230, G.231, E.232, E.235, N.258, N.260, Q.262, R.263, L.264, K.392, H.407 Chain B: D.521, E.522, I.569, E.571, Y.599, F.602, R.606, E.636, H.640 Ligands: MG.5 21 PLIP interactions: 18 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:S.109, A:Q.140, A:Y.177, A:V.192, A:M.194, A:G.229, A:D.230, A:G.231, A:E.232, A:N.258, A:N.260, B:Y.599 Water bridges: A:G.229, A:E.232, A:Q.408 Salt bridges: A:H.142, A:K.392, A:K.392, A:H.407 Hydrophobic interactions: B:F.602 pi-Stacking: B:F.602

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Arjunan, P. et al., A Thiamin-bound, Pre-decarboxylation Reaction Intermediate Analogue in the Pyruvate Dehydrogenase E1 Subunit Induces Large Scale Disorder-to-Order Transformations in the Enzyme and Reveals Novel Structural Features in the Covalently Bound Adduct. J.Biol.Chem. (2006)

Release Date

2006-04-25

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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