SMTL ID : 6hg8.1

Crystal structure of the R460G disease-causing mutant of the human dihydrolipoamide dehydrogenase.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.76 Å

Oligo State

homo-dimer

Ligands

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

FAD.1: 38 residues within 4Å: Chain A: I.34, G.35, 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, G.341, D.342, M.348, L.349, A.350, H.351, A.353, Y.381 Chain B: H.474, P.475 30 PLIP interactions: 28 interactions with chain A, 2 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: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:K.59, A:N.60, 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.8: 39 residues within 4Å: Chain A: H.474, P.475 Chain B: 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, G.341, D.342, M.348, L.349, A.350, H.351, A.353, Y.381 31 PLIP interactions: 28 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:T.66, B:I.211, B:I.211 Hydrogen bonds: B:G.37, B:G.39, B:G.40, B:K.59, B:T.66, B:T.66, B:T.66, B:C.67, B:S.75, B:K.76, B:G.141, B:G.141, B:S.172, B:D.342, B:M.348, B:A.350, A:H.474 Water bridges: B:K.59, B:K.59, B:K.59, B:N.60, B:N.60, B:G.65, B:S.172, B:V.343, A:H.474, A:H.474 pi-Cation interactions: B:K.59

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

SO4.2: 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 SO4.3: 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 SO4.4: 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:N.308, A:L.309, A:G.310, A:L.311, A:E.312 Water bridges: A:T.306 SO4.5: 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 SO4.6: 3 residues within 4Å: Chain A: H.86, G.90, K.91 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.91 Water bridges: A:G.90, A:D.92 Salt bridges: A:H.86 SO4.9: 2 residues within 4Å: Chain B: G.209, G.237 2 PLIP interactions: 2 interactions with chain B Water bridges: B:G.209, B:V.210 SO4.10: 4 residues within 4Å: Chain A: E.449 Chain B: R.415, N.419, L.477 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.419 Water bridges: B:R.415 Salt bridges: B:R.415 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: 6 residues within 4Å: Chain B: 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 SO4.13: 3 residues within 4Å: Chain B: H.86, G.90, K.91 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.91 Salt bridges: B:H.86, B:K.91 SO4.14: 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

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.7: 3 residues within 4Å: Chain A: K.271, S.272, D.273 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.272, A:D.273, A:D.273

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ambrus, A. et al., Crystal structure of the R460G disease-causing mutant of the human dihydrolipoamide dehydrogenase. To Be Published

Release Date

2019-09-04

Peptides

Dihydrolipoyl dehydrogenase, mitochondrial: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Dihydrolipoyl dehydrogenase, mitochondrial

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