SMTL ID : 5j5z.1

Crystal structure of the D444V disease-causing mutant of the human dihydrolipoamide dehydrogenase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.84 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, 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, L.309, G.341, D.342, M.348, L.349, A.350, H.351, A.353, Y.381 Chain B: H.474, P.475 29 PLIP interactions: 27 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:T.66, A:I.211, A:I.211, A:I.211 Hydrogen bonds: A:G.37, A:G.39, A:G.40, 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, A:H.351, B:H.474 Water bridges: A:G.65, A:G.171, A:S.172, A:V.343, A:Y.381, B:H.474 pi-Cation interactions: A:K.59 FAD.6: 40 residues within 4Å: Chain A: H.474, P.475 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, 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 30 PLIP interactions: 27 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:T.66, B:I.211, B:I.211, B:I.211 Hydrogen bonds: B:G.37, B:G.39, B:G.40, B:K.59, B:N.60, B:T.66, 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 Water bridges: B:N.60, B:G.65, B:S.172, B:V.343, B:A.353, A:H.474, A:H.474 pi-Cation interactions: B:K.59

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.2: 4 residues within 4Å: Chain A: R.321, R.323, A.345, G.346 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.346 Water bridges: A:R.321, A:R.321 Salt bridges: A:R.321, A:R.323 PO4.7: 4 residues within 4Å: Chain B: R.321, R.323, A.345, G.346 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.346 Salt bridges: B:R.321, B:R.323

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 7 residues within 4Å: Chain A: T.306, N.308, L.309, G.310, L.311, E.312, E.313 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.306, A:L.309, A:G.310, A:L.311, A:E.312 Water bridges: A:K.142 GOL.4: 3 residues within 4Å: Chain A: Q.431, S.433, T.434 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.431, A:S.433 GOL.5: 8 residues within 4Å: Chain A: D.355, H.370, I.371, D.372, C.375, E.459 Chain B: R.469, C.471 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:R.469, A:D.372, A:D.372 Water bridges: B:C.471, B:R.482, B:R.482

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

2017-11-15

Peptides

Dihydrolipoyl dehydrogenase, mitochondrial: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Dihydrolipoyl dehydrogenase, mitochondrial