SMTL ID : 1umd.1

branched-chain 2-oxo acid dehydrogenase (E1) from Thermus thermophilus HB8 with 4-methyl-2-oxopentanoate as an intermediate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

hetero-oligomer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: D.175, N.204, Y.206 Ligands: TDP.3 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.175, A:Y.206, H2O.32 MG.2: 4 residues within 4Å: Chain C: D.175, N.204, Y.206 Ligands: TDP.5 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.175, C:Y.206, H2O.666

2 x TDP: THIAMIN DIPHOSPHATE(Non-covalent)

TDP.3: 24 residues within 4Å: Chain A: Y.94, Y.95, R.96, S.144, P.145, I.146, G.174, D.175, G.176, A.177, E.180, N.204, Y.206, A.207, I.208, H.273 Chain D: E.29, L.58, E.60, Q.82, Y.86, P.89 Ligands: MG.1, COI.4 19 PLIP interactions: 16 interactions with chain A, 3 interactions with chain D Hydrophobic interactions: A:I.208, A:I.208, D:Y.86, D:P.89 Hydrogen bonds: A:Y.95, A:Y.95, A:S.144, A:I.146, A:G.174, A:D.175, A:G.176, A:A.177, A:N.204 Water bridges: A:N.204, A:I.208, A:I.208 Salt bridges: A:R.96, A:H.273 pi-Stacking: D:Y.86 TDP.5: 24 residues within 4Å: Chain B: E.29, L.58, E.60, Q.82, Y.86, P.89 Chain C: Y.94, Y.95, R.96, S.144, P.145, I.146, G.174, D.175, G.176, A.177, E.180, N.204, Y.206, A.207, I.208, H.273 Ligands: MG.2, COI.6 19 PLIP interactions: 16 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: C:I.208, C:I.208, B:Y.86, B:P.89 Hydrogen bonds: C:Y.95, C:Y.95, C:S.144, C:I.146, C:G.174, C:D.175, C:G.176, C:A.177, C:N.204, C:N.204 Water bridges: C:I.208, C:I.208 Salt bridges: C:R.96, C:H.273 pi-Stacking: B:Y.86

2 x COI: 2-OXO-4-METHYLPENTANOIC ACID(Non-covalent)

COI.4: 7 residues within 4Å: Chain A: F.66, Y.95, H.131, S.144 Chain D: Y.86, H.129 Ligands: TDP.3 5 PLIP interactions: 2 interactions with chain D, 3 interactions with chain A Hydrogen bonds: D:Y.86, D:H.129 Hydrophobic interactions: A:F.66, A:Y.95, A:Y.95 COI.6: 6 residues within 4Å: Chain B: Y.86, H.129 Chain C: F.66, Y.95, S.144 Ligands: TDP.5 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:H.129 Hydrophobic interactions: C:F.66, C:Y.95

Links

RCSB   PDBe   PDBj   PDBsum   CATH   PLIP

Citation

Nakai, T. et al., Ligand-induced Conformational Changes and a Reaction Intermediate in Branched-chain 2-Oxo Acid Dehydrogenase (E1) from Thermus thermophilus HB8, as Revealed by X-ray Crystallography. J.Mol.Biol. (2004)

Release Date

2004-03-30

Peptides

2-oxo acid dehydrogenase alpha subunit: AC
2-oxo acid dehydrogenase beta subunit: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

2-oxo acid dehydrogenase alpha subunit

2-oxo acid dehydrogenase beta subunit

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