SMTL ID : 1zmc.4 (3 other biounits)

Crystal Structure of Human dihydrolipoamide dehydrogenase complexed to NAD+

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.53 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 3 residues within 4Å: Chain A: H.64, G.68, T.69 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.64, A:T.69, A:T.69 Water bridges: A:D.70 Salt bridges: A:H.64 SO4.2: 7 residues within 4Å: Chain A: T.284, N.286, L.287, G.288, L.289, E.290, E.291 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.286, A:L.287, A:G.288, A:L.289, A:E.290 SO4.3: 4 residues within 4Å: Chain A: G.378, I.379, E.380, Q.409 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.380, A:E.380, A:Q.409 SO4.4: 2 residues within 4Å: Chain A: R.299, R.301 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.299, A:R.301 SO4.5: 4 residues within 4Å: Chain A: L.210, G.211, H.212, M.220 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.211 Salt bridges: A:H.212 SO4.8: 3 residues within 4Å: Chain B: H.64, G.68, T.69 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:T.69, B:T.69 Water bridges: B:D.70, B:D.70 Salt bridges: B:H.64 SO4.9: 6 residues within 4Å: Chain B: N.286, L.287, G.288, L.289, E.290, E.291 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.286, B:L.287, B:G.288, B:L.289, B:E.290 SO4.10: 5 residues within 4Å: Chain B: G.378, I.379, E.380, Q.409, S.411 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:G.378, B:E.380, B:Q.409, B:S.411, B:S.411 SO4.11: 4 residues within 4Å: Chain B: R.299, R.301, A.323, G.324 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.324 Salt bridges: B:R.299, B:R.301 SO4.12: 4 residues within 4Å: Chain B: L.210, G.211, H.212, M.220 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.211 Salt bridges: B:H.212

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

FAD.6: 39 residues within 4Å: Chain A: I.12, G.13, S.14, G.15, P.16, G.17, I.35, E.36, K.37, N.38, G.43, T.44, C.45, V.48, G.49, C.50, S.53, K.54, G.117, Y.118, G.119, A.147, T.148, G.149, S.150, S.168, I.189, R.280, F.283, L.287, G.319, D.320, M.326, L.327, A.328, H.329, A.331, Y.359 Chain B: H.452 29 PLIP interactions: 26 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:I.189, A:I.189 Hydrogen bonds: A:G.17, A:G.18, A:K.37, A:N.38, A:T.44, A:T.44, A:T.44, A:C.45, A:S.53, A:K.54, A:G.119, A:G.119, A:S.150, A:D.320, A:M.326, A:A.328, A:H.329, B:H.452 Water bridges: A:G.15, A:G.15, A:K.37, A:N.38, A:G.43, A:V.321, B:H.452, B:H.452 pi-Cation interactions: A:K.37 FAD.13: 40 residues within 4Å: Chain A: H.452, P.453 Chain B: I.12, G.13, S.14, G.15, P.16, G.17, G.18, I.35, E.36, K.37, N.38, G.43, T.44, C.45, V.48, G.49, C.50, S.53, K.54, G.117, Y.118, G.119, A.147, T.148, G.149, S.150, S.168, I.189, R.280, F.283, G.319, D.320, M.326, L.327, A.328, H.329, A.331, Y.359 26 PLIP interactions: 25 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:I.189, B:I.189 Hydrogen bonds: B:G.17, B:G.18, B:K.37, B:K.37, B:N.38, B:N.38, B:T.44, B:T.44, B:C.45, B:K.54, B:G.119, B:G.119, B:S.150, B:D.320, B:M.326, B:A.328, B:H.329, A:H.452 Water bridges: B:G.15, B:G.43, B:G.149, B:S.150, B:Y.359 pi-Cation interactions: B:K.37

2 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.7: 16 residues within 4Å: Chain A: F.155, I.184, G.185, A.186, G.187, V.207, E.208, F.209, L.210, V.216, T.241, K.242, V.243, C.277, I.278, G.279 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:F.209, A:V.216, A:V.243, A:V.243 Water bridges: A:A.186, A:G.187, A:G.187, A:E.208, A:R.280 NAD.14: 15 residues within 4Å: Chain B: F.155, G.185, G.187, V.207, E.208, F.209, L.210, G.215, V.216, T.241, K.242, V.243, C.277, I.278, G.279 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:G.187, B:F.209, B:V.216, B:V.243, B:V.243 Water bridges: B:A.186, B:G.214, B:G.215, B:V.216, B:R.280

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Brautigam, C.A. et al., Crystal Structure of Human Dihydrolipoamide Dehydrogenase: NAD(+)/NADH Binding and the Structural Basis of Disease-causing Mutations. J.Mol.Biol. (2005)

Release Date

2005-06-28

Peptides

Dihydrolipoyl dehydrogenase, mitochondrial: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

B
H

Dihydrolipoyl dehydrogenase, mitochondrial

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