SMTL ID : 2f5z.2 (4 other biounits)

Crystal Structure of Human Dihydrolipoamide Dehydrogenase (E3) Complexed to the E3-Binding Domain of Human E3-Binding Protein

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.18 Å

Oligo State

hetero-2-1-mer

Ligands

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

SO4.1: 4 residues within 4Å: Chain A: R.299, R.301, A.323, G.324 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.324 Salt bridges: A:R.299, A:R.301 SO4.2: 4 residues within 4Å: Chain A: H.64, G.68, T.69, D.70 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.69, A:D.70 Water bridges: A:H.64, A:H.64, A:G.68 Salt bridges: A:H.64 SO4.3: 4 residues within 4Å: Chain A: L.210, G.211, H.212, M.220 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.211 Water bridges: A:N.240 Salt bridges: A:H.212 SO4.4: 7 residues within 4Å: Chain A: T.284, N.286, L.287, G.288, L.289, E.290, E.291 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:T.284, A:N.286, A:L.287, A:G.288, A:L.289, A:E.290, A:E.291 SO4.6: 4 residues within 4Å: Chain B: R.299, R.301, A.323, G.324 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:G.324, B:G.324 Water bridges: B:R.301, B:R.301 Salt bridges: B:R.299, B:R.301 SO4.7: 3 residues within 4Å: Chain B: H.64, G.68, T.69 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.69, B:D.70 Salt bridges: B:H.64 SO4.8: 3 residues within 4Å: Chain B: L.210, G.211, H.212 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.211, B:G.211 Salt bridges: B:H.212 SO4.9: 6 residues within 4Å: Chain B: T.284, N.286, L.287, G.288, L.289, E.290 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:T.284, B:N.286, B:L.287, B:G.288, B:L.289, B:E.290

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

FAD.5: 40 residues within 4Å: Chain A: I.12, G.13, S.14, G.15, P.16, G.17, G.18, I.35, E.36, K.37, N.38, G.43, T.44, C.45, V.48, G.49, C.50, S.53, K.54, G.117, Y.118, G.119, A.147, T.148, G.149, S.150, S.168, I.189, R.280, F.283, G.319, D.320, M.326, L.327, A.328, H.329, A.331, Y.359 Chain B: H.452, P.453 38 PLIP interactions: 35 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:T.44, A:I.189, A:I.189, A:I.189 Hydrogen bonds: A:S.14, A:G.17, A:G.18, A:K.37, A:N.38, A:T.44, A:T.44, A:T.44, A:C.45, A:K.54, A:G.119, A:G.119, A:S.150, A:D.320, A:M.326, A:A.328, A:H.329, A:H.329, B:H.452 Water bridges: A:G.15, A:K.37, A:K.37, A:K.37, A:N.38, A:G.43, A:Y.118, A:Y.118, A:G.149, A:S.150, A:V.321, A:A.331, B:H.452, B:H.452 pi-Cation interactions: A:K.37 FAD.10: 40 residues within 4Å: Chain A: H.452, P.453 Chain B: I.12, G.13, S.14, G.15, P.16, G.17, I.35, E.36, K.37, N.38, G.43, T.44, C.45, V.48, G.49, C.50, S.53, K.54, G.117, Y.118, G.119, A.147, T.148, G.149, S.150, S.168, I.189, R.280, F.283, L.287, G.319, D.320, M.326, L.327, A.328, H.329, A.331, Y.359 35 PLIP interactions: 32 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:T.44, B:I.189, B:I.189, B:I.189 Hydrogen bonds: B:G.17, B:G.18, B:K.37, B:N.38, B:N.38, B:T.44, B:T.44, B:C.45, B:K.54, B:G.119, B:G.119, B:S.150, B:D.320, B:M.326, B:A.328, B:H.329, B:H.329, A:H.452 Water bridges: B:G.15, B:G.15, B:G.43, B:N.47, B:Y.118, B:Y.118, B:G.149, B:S.150, B:V.321, B:A.331, A:H.452, A:H.452 pi-Cation interactions: B:K.37

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Brautigam, C.A. et al., Structural Insight into Interactions between Dihydrolipoamide Dehydrogenase (E3) and E3 Binding Protein of Human Pyruvate Dehydrogenase Complex. Structure (2006)

Release Date

2006-01-17

Peptides

Dihydrolipoyl dehydrogenase: AB
Pyruvate dehydrogenase protein X component: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

C
L

Dihydrolipoyl dehydrogenase

Pyruvate dehydrogenase protein X component

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