SMTL ID : 7psc.1

Crystal structure of the disease-causing I358T mutant of the human dihydrolipoamide dehydrogenase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.44 Å

Oligo State

homo-dimer

Ligands

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

FAD.1: 40 residues within 4Å: Chain A: I.34, G.35, S.36, G.37, P.38, G.39, G.40, I.57, E.58, K.59, N.60, G.65, T.66, C.67, V.70, G.71, C.72, S.75, K.76, G.139, Y.140, G.141, A.169, T.170, G.171, S.172, S.190, I.211, R.302, F.305, G.341, D.342, M.348, L.349, A.350, H.351, A.353, Y.381 Chain B: H.474 Ligands: BTB.2 26 PLIP interactions: 25 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:T.66, A:I.211, A:I.211, A:I.211 Hydrogen bonds: A:S.36, A:G.39, A:G.40, A:E.58, A:K.59, A:K.59, A:N.60, A:T.66, A:T.66, A:T.66, A:C.67, A:K.76, A:G.141, A:G.141, A:S.172, A:D.342, A:D.342, A:M.348, A:A.350, A:H.351, B:H.474 pi-Cation interactions: A:K.59 FAD.4: 40 residues within 4Å: Chain A: H.474 Chain B: I.34, G.35, S.36, G.37, P.38, G.39, G.40, I.57, E.58, K.59, N.60, G.65, T.66, C.67, G.71, C.72, S.75, K.76, G.139, Y.140, G.141, A.169, T.170, G.171, S.172, S.190, I.211, R.302, F.305, L.309, G.341, D.342, M.348, L.349, A.350, H.351, A.353, Y.381 Ligands: BTB.5 24 PLIP interactions: 23 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:T.66, B:I.211, B:I.211 Hydrogen bonds: B:S.36, B:G.39, B:G.40, B:K.59, B:N.60, B:N.60, B:N.60, B:G.65, B:T.66, B:T.66, B:C.67, B:K.76, B:G.141, B:G.141, B:S.172, B:D.342, B:D.342, B:M.348, B:A.350, B:H.351, A:H.474

4 x BTB: 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-covalent)

BTB.2: 9 residues within 4Å: Chain A: K.59, N.60, T.66, T.170, S.172, E.173, R.302, F.305 Ligands: FAD.1 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:K.59, A:N.60, A:T.66, A:T.170, A:S.172, A:E.173, A:R.302, A:R.302 BTB.3: 4 residues within 4Å: Chain A: Y.460, G.461, D.466 Chain B: Y.460 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.460 Salt bridges: A:D.466 BTB.5: 9 residues within 4Å: Chain B: K.59, N.60, T.66, T.170, S.172, E.173, T.191, F.305 Ligands: FAD.4 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:K.59, B:N.60, B:T.66, B:T.170, B:S.172, B:E.173, B:E.173, B:T.191, B:T.191 BTB.6: 5 residues within 4Å: Chain A: Y.460 Chain B: Y.460, G.461, S.463, D.466 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Y.460, A:Y.460 Salt bridges: B:D.466

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Szabo, E. et al., Structural and Biochemical Investigation of Selected Pathogenic Mutants of the Human Dihydrolipoamide Dehydrogenase. Int J Mol Sci (2023)

Release Date

2023-04-05

Peptides

Dihydrolipoyl dehydrogenase, mitochondrial: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Dihydrolipoyl dehydrogenase, mitochondrial