SMTL ID : 4jdr.1

Dihydrolipoamide dehydrogenase of pyruvate dehydrogenase from escherichia coli

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

2 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)

FAD.1: 37 residues within 4Å: Chain A: L.12, G.13, A.14, G.15, P.16, A.17, V.35, E.36, R.37, Y.38, G.43, V.44, C.45, V.48, G.49, C.50, K.54, G.115, L.116, G.117, A.144, A.145, G.146, S.147, S.165, I.186, R.273, L.280, G.312, D.313, M.319, L.320, A.321, H.322, Y.352 Chain B: H.445, P.446 27 PLIP interactions: 25 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:V.44, A:I.186, A:I.186 Hydrogen bonds: A:A.14, A:G.15, A:A.17, A:G.18, A:R.37, A:V.44, A:C.45, A:K.54, A:G.117, A:G.117, A:S.147, A:D.313, A:M.319, A:A.321, A:H.322, A:H.322, B:H.445 Water bridges: A:R.37, A:G.43, A:G.146, A:D.313, A:Y.352, B:H.445 pi-Cation interactions: A:R.37 FAD.9: 37 residues within 4Å: Chain A: H.445 Chain B: L.12, G.13, A.14, G.15, P.16, A.17, G.18, V.35, E.36, R.37, Y.38, G.43, V.44, C.45, V.48, G.49, C.50, K.54, G.115, L.116, G.117, A.144, A.145, G.146, S.147, S.165, I.186, R.273, L.280, G.312, D.313, M.319, L.320, A.321, H.322, Y.352 28 PLIP interactions: 25 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:V.44, B:I.186, B:I.186 Hydrogen bonds: B:A.14, B:G.15, B:A.17, B:G.18, B:R.37, B:R.37, B:V.44, B:C.45, B:K.54, B:G.117, B:G.117, B:S.147, B:D.313, B:M.319, B:A.321, B:H.322, B:H.322, A:H.445 Water bridges: B:A.14, B:R.37, B:G.43, B:D.313, A:H.445, A:H.445 pi-Cation interactions: B:R.37

3 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.2: 11 residues within 4Å: Chain A: G.184, I.185, I.211, P.212, A.213, Q.317, P.318, M.319, L.320 Ligands: MES.3, SO4.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:M.319 MES.3: 10 residues within 4Å: Chain A: G.182, G.184, V.204, E.205, M.206, P.212, A.270, I.271 Ligands: MES.2, SO4.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:M.206 Salt bridges: A:E.205 MES.10: 6 residues within 4Å: Chain B: G.184, I.185, I.186, I.211, P.212, A.213 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:I.185, B:I.186, B:A.213 Water bridges: B:G.184, B:G.187, B:R.273

7 x SO4: SULFATE ION(Non-functional Binders)

SO4.4: 7 residues within 4Å: Chain A: G.184, I.185, I.186, A.270, G.272 Ligands: MES.2, MES.3 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:I.185, A:I.186 Water bridges: A:G.187, A:R.273 SO4.5: 4 residues within 4Å: Chain A: D.281, A.282, G.283, V.289 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.283 Water bridges: A:V.289 SO4.6: 1 residues within 4Å: Chain A: R.263 4 PLIP interactions: 4 interactions with chain A Water bridges: A:R.177, A:R.177, A:R.263 Salt bridges: A:R.263 SO4.7: 2 residues within 4Å: Chain A: D.298, K.299 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.299 Salt bridges: A:K.299 SO4.8: 3 residues within 4Å: Chain A: Y.374, E.375, T.376 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.376 SO4.11: 1 residues within 4Å: Chain B: R.263 2 PLIP interactions: 2 interactions with chain B Water bridges: B:R.263 Salt bridges: B:R.263 SO4.12: 4 residues within 4Å: Chain B: G.121, A.122, N.123, T.124 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:A.122, B:N.123, B:T.124

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chandrasekhar, K. et al., Insight to the Interaction of the Dihydrolipoamide Acetyltransferase (E2) Core with the Peripheral Components in the Escherichia coli Pyruvate Dehydrogenase Complex via Multifaceted Structural Approaches. J.Biol.Chem. (2013)

Release Date

2013-04-24

Peptides

Dihydrolipoyl dehydrogenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Dihydrolipoyl dehydrogenase

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