SMTL ID : 6i4q.1

Crystal structure of the human dihydrolipoamide dehydrogenase at 1.75 Angstrom resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 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.2 33 PLIP interactions: 30 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:T.66, A:I.211, A:I.211 Hydrogen bonds: A:G.37, A:G.39, A:G.40, A:E.58, A:E.58, 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:M.348, A:A.350, A:H.351, B:H.474 Water bridges: A:S.36, A:Y.140, A:Y.140, A:G.171, A:S.172, A:V.343, B:H.474, B:H.474 FAD.9: 44 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, L.309, G.341, D.342, M.348, L.349, A.350, H.351, A.353, Y.381 Ligands: BTB.10 33 PLIP interactions: 30 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:I.211, B:I.211 Hydrogen bonds: B:S.36, B:G.37, B:G.39, B:G.40, B:E.58, B:E.58, B:K.59, B:K.59, 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:M.348, B:A.350, B:H.351, A:H.474 Water bridges: B:S.36, B:Y.140, B:Y.140, B:G.171, B:S.172, B:V.343, A:H.474, A:H.474

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

BTB.2: 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 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:K.59, A:N.60, A:R.302 Water bridges: A:S.172, A:V.174, A:R.302 BTB.10: 10 residues within 4Å: Chain B: K.59, N.60, T.66, V.70, S.172, E.173, V.174, R.302, F.305 Ligands: FAD.9 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:K.59, B:N.60, B:T.66, B:R.302 Water bridges: B:T.170

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

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:T.306, A:N.308, A:L.309, A:G.310, A:L.311, A:E.312 Water bridges: A:G.310, A:E.313 SO4.4: 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 SO4.5: 4 residues within 4Å: Chain A: H.86, G.90, K.91, D.92 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.91 Water bridges: A:H.86 Salt bridges: A:H.86 SO4.6: 3 residues within 4Å: Chain A: L.232, G.233, H.234 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.233, A:G.233 Salt bridges: A:H.234 SO4.7: 2 residues within 4Å: Chain A: P.176, R.303 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.303 SO4.8: 3 residues within 4Å: Chain A: K.146, P.335, N.336 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.336 Salt bridges: A:K.146 SO4.11: 7 residues within 4Å: Chain B: K.142, T.306, N.308, L.309, G.310, L.311, E.312 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:N.308, B:L.309, B:G.310, B:L.311, B:E.312 Water bridges: B:K.142 SO4.12: 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 SO4.13: 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 SO4.14: 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

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