SMTL ID : 2g28.1

E. Coli Pyruvate Dehydrogenase H407A variant Phosphonolactylthiamin Diphosphate Complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 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.2 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.230, B:Q.262, H2O.1 MG.3: 4 residues within 4Å: Chain A: D.230, N.260, Q.262 Ligands: TDK.4 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.230, A:Q.262, H2O.1

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.2: 29 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 Ligands: MG.1 21 PLIP interactions: 19 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:S.109, 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 pi-Stacking: B:H.142 Hydrophobic interactions: A:F.602 TDK.4: 28 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, K.392 Chain B: D.521, E.522, I.569, E.571, Y.599, F.602, R.606, E.636, H.640 Ligands: MG.3 22 PLIP interactions: 19 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:M.194, B:F.602 Hydrogen bonds: A:S.109, 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 Salt bridges: A:H.142, A:K.392, A:K.392 pi-Stacking: A:H.142, 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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