SMTL ID : 6i4r.1

Crystal structure of the disease-causing R460G mutant of the human dihydrolipoamide dehydrogenase at 1.44 Angstrom resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.44 Å

Oligo State

homo-dimer

Ligands

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

FAD.1: 45 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, L.194, I.211, L.215, R.302, F.305, K.307, L.309, G.341, D.342, M.348, L.349, A.350, H.351, A.353, Y.381 Chain B: H.474, P.475 Ligands: BTB.6 32 PLIP interactions: 29 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:I.211, A:I.211 Hydrogen bonds: A:G.37, A:G.39, A:G.40, A:K.59, A:K.59, A:N.60, A:G.65, 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:A.350, A:H.351, B:H.474 Water bridges: A:S.36, A:S.36, A:Y.140, A:Y.140, A:G.171, A:S.172, A:V.343, B:H.474, B:H.474 pi-Cation interactions: A:K.59 FAD.7: 45 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, L.194, I.211, L.215, R.302, F.305, K.307, L.309, G.341, D.342, M.348, L.349, A.350, H.351, A.353, Y.381 Ligands: BTB.13 32 PLIP interactions: 3 interactions with chain A, 29 interactions with chain B Hydrogen bonds: A:H.474, B:G.37, B:G.39, B:G.40, B:E.58, B:K.59, B:K.59, B:N.60, B:N.60, B:G.65, 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:L.349, B:A.350 Water bridges: A:H.474, A:H.474, B:S.36, B:Y.140, B:Y.140, B:G.171, B:S.172, B:V.343 Hydrophobic interactions: B:I.211, B:I.211 pi-Cation interactions: B:K.59

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

SO4.2: 4 residues within 4Å: Chain A: R.321, R.323, A.345, G.346 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.346 Water bridges: A:R.323 Salt bridges: A:R.321, A:R.323 SO4.3: 8 residues within 4Å: Chain A: K.142, T.306, K.307, N.308, L.309, G.310, L.311, E.312 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:N.308, A:L.309, A:G.310, A:L.311, A:E.312 Water bridges: A:T.306, A:E.312, A:E.313 SO4.4: 4 residues within 4Å: Chain A: H.86, G.90, K.91, D.92 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.91 Water bridges: A:H.86, A:D.92, A:D.92 Salt bridges: A:H.86 SO4.5: 4 residues within 4Å: Chain A: L.232, G.233, H.234, M.242 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.233 Salt bridges: A:H.234 SO4.8: 7 residues within 4Å: Chain B: K.142, T.306, N.308, L.309, G.310, L.311, E.312 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:N.308, B:L.309, B:G.310, B:L.311, B:E.312 Water bridges: B:G.310, B:E.313 SO4.9: 4 residues within 4Å: Chain B: H.86, G.90, K.91, D.92 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.91 Water bridges: B:D.92, B:D.92 Salt bridges: B:H.86 SO4.10: 4 residues within 4Å: Chain B: R.321, R.323, A.345, G.346 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.346 Water bridges: B:R.323 Salt bridges: B:R.321, B:R.323 SO4.11: 3 residues within 4Å: Chain B: L.232, G.233, H.234 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.233 Salt bridges: B:H.234 SO4.12: 1 residues within 4Å: Chain B: R.436 5 PLIP interactions: 5 interactions with chain B Water bridges: B:R.436, B:R.436, B:R.436, B:R.436 Salt bridges: B:R.436

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

BTB.6: 11 residues within 4Å: Chain A: K.59, N.60, G.65, T.66, V.70, S.172, E.173, V.174, R.302, F.305 Ligands: FAD.1 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:K.59, A:N.60, A:N.60, A:R.302 Water bridges: A:T.170, A:V.174, A:R.302 BTB.13: 11 residues within 4Å: Chain B: K.59, N.60, G.65, T.66, V.70, S.172, E.173, V.174, R.302, F.305 Ligands: FAD.7 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:K.59, B:N.60, B:R.302 Water bridges: B:T.170, B:V.174, B:R.302

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Szabo, E. et al., Underlying molecular alterations in human dihydrolipoamide dehydrogenase deficiency revealed by structural analyses of disease-causing enzyme variants. Hum.Mol.Genet. (2019)

Release Date

2019-11-20

Peptides

Dihydrolipoyl dehydrogenase, mitochondrial: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Dihydrolipoyl dehydrogenase, mitochondrial

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