SMTL ID : 5nhg.3 (3 other biounits)

Crystal structure of the human dihydrolipoamide dehydrogenase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.27 Å

Oligo State

homo-dimer

Ligands

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

FAD.1: 46 residues within 4Å: Chain A: I.33, G.34, S.35, G.36, P.37, G.38, G.39, I.56, E.57, K.58, N.59, G.64, T.65, C.66, V.69, G.70, C.71, S.74, K.75, G.138, Y.139, G.140, A.168, T.169, G.170, S.171, S.189, L.193, I.210, E.213, L.214, R.301, F.304, K.306, L.308, G.340, D.341, M.347, L.348, A.349, H.350, A.352, Y.380 Chain B: H.473, P.474 Ligands: TRS.2 26 PLIP interactions: 25 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:I.210, A:I.210 Hydrogen bonds: A:S.35, A:G.36, A:G.38, A:G.39, A:K.58, A:K.58, A:N.59, A:N.59, A:G.64, A:T.65, A:T.65, A:T.65, A:C.66, A:K.75, A:G.140, A:G.140, A:S.171, A:D.341, A:L.348, A:A.349, A:H.350, B:H.473 Water bridges: A:V.342 pi-Cation interactions: A:K.58 FAD.4: 45 residues within 4Å: Chain A: H.473, P.474 Chain B: I.33, G.34, S.35, G.36, P.37, G.38, G.39, I.56, E.57, K.58, N.59, G.64, T.65, C.66, V.69, G.70, C.71, S.74, K.75, G.138, Y.139, G.140, A.168, T.169, G.170, S.171, S.189, L.193, I.210, L.214, R.301, F.304, K.306, L.308, G.340, D.341, M.347, L.348, A.349, H.350, A.352, Y.380 Ligands: TRS.5 25 PLIP interactions: 1 interactions with chain A, 24 interactions with chain B Hydrogen bonds: A:H.473, B:S.35, B:G.36, B:G.38, B:G.39, B:K.58, B:K.58, B:G.64, B:T.65, B:T.65, B:T.65, B:C.66, B:K.75, B:G.140, B:G.140, B:S.171, B:D.341, B:L.348, B:A.349 Hydrophobic interactions: B:T.65, B:I.210, B:I.210 Water bridges: B:G.170, B:V.342 pi-Cation interactions: B:K.58

3 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.2: 7 residues within 4Å: Chain A: K.58, N.59, T.65, V.69, E.172, R.301 Ligands: FAD.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.58, A:N.59, A:N.59, A:T.65, A:R.301 TRS.3: 10 residues within 4Å: Chain A: G.238, P.346, Y.372, N.373, V.375, S.377, W.387, V.388, G.389, Q.394 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Y.372, A:N.373, A:V.375, A:S.377, A:W.387, A:G.389, A:Q.394 TRS.5: 9 residues within 4Å: Chain B: K.58, N.59, T.65, V.69, S.171, E.172, V.173, R.301 Ligands: FAD.4 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:K.58, B:N.59, B:N.59, B:S.171, B:V.173, B:R.301, B:R.301 Water bridges: B:S.171

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Szabo, E. et al., Crystal structures of the disease-causing D444V mutant and the relevant wild type human dihydrolipoamide dehydrogenase. Free Radic. Biol. Med. (2018)

Release Date

2018-05-16

Peptides

Dihydrolipoyl dehydrogenase, mitochondrial: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
F

Dihydrolipoyl dehydrogenase, mitochondrial

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