SMTL ID : 7zyt.1

Crystal structure of the I318T pathogenic variant of the human dihydrolipoamide dehydrogenase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.89 Å

Oligo State

homo-dimer

Ligands

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

FAD.1: 39 residues within 4Å: Chain A: I.34, G.35, S.36, G.37, P.38, G.39, 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, L.309, G.341, D.342, M.348, L.349, A.350, H.351, Y.381 Chain B: H.474, P.475 22 PLIP interactions: 21 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:I.211, A:I.211, A:I.211 Hydrogen bonds: A:S.36, A:S.36, A:G.37, A:G.39, A:K.59, A:N.60, 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:M.348, A:A.350, A:H.351, B:H.474 pi-Cation interactions: A:K.59 FAD.3: 36 residues within 4Å: Chain A: H.474, P.475 Chain B: I.34, G.35, S.36, G.37, P.38, G.39, 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, F.305, D.342, M.348, L.349, A.350, H.351, A.353, Y.381 20 PLIP interactions: 19 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:I.211, B:I.211 Hydrogen bonds: B:S.36, B:G.37, B:G.39, B:K.59, B:N.60, 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:M.348, B:A.350, B:H.351, A:H.474 pi-Cation interactions: B:K.59

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

BTB.2: 4 residues within 4Å: Chain A: G.461, S.463, E.465, D.466 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.463, A:S.463, A:E.465 Salt bridges: A:D.466 BTB.5: 5 residues within 4Å: Chain A: Y.460 Chain B: G.461, A.462, S.463, D.466 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Y.460, B:G.461, B:S.463, B:S.463, B:S.463, A:Y.460 Salt bridges: B:D.466

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 4 residues within 4Å: Chain B: K.271, D.273, K.275, T.292 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.271, B:K.271, B:D.273

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

2023-06-14

Peptides

Dihydrolipoyl dehydrogenase, mitochondrial: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Dihydrolipoyl dehydrogenase, mitochondrial