SMTL ID : 9jq3.1

Structure of human IVD in complex with FAD

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

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

FAD.1: 34 residues within 4Å: Chain A: L.127, L.135, L.165, A.166, M.167, S.168, G.173, S.174, W.198, T.200, K.245, T.253, L.402, I.405, G.406, A.407, G.408, T.409, E.411, V.412, L.415 Chain B: R.312, A.314, F.315, I.319, F.322, L.324, M.325, Q.380, C.381, F.382, G.383, G.384 Chain D: Q.323 17 PLIP interactions: 12 interactions with chain A, 1 interactions with chain D, 4 interactions with chain B Hydrophobic interactions: A:L.135, A:W.198 Hydrogen bonds: A:G.173, A:G.173, A:S.174, A:T.253, A:I.405, A:A.407, A:G.408, A:T.409, A:E.411, A:E.411, D:Q.323, B:G.384 Salt bridges: B:R.312, B:R.312 pi-Stacking: B:F.322 FAD.2: 34 residues within 4Å: Chain A: R.312, A.314, F.315, I.319, F.322, L.324, M.325, Q.380, C.381, F.382, G.383, G.384, Y.387 Chain B: L.127, L.135, L.165, A.166, M.167, S.168, G.173, S.174, W.198, T.200, K.245, T.253, L.402, I.405, G.406, A.407, G.408, T.409, E.411, L.415 Chain C: Q.323 13 PLIP interactions: 8 interactions with chain B, 4 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: B:L.135 Hydrogen bonds: B:S.168, B:T.253, B:G.406, B:G.408, B:T.409, B:E.411, B:E.411, A:G.384, C:Q.323 Salt bridges: A:R.312, A:R.312 pi-Stacking: A:F.322 FAD.3: 33 residues within 4Å: Chain B: Q.323 Chain C: L.127, A.131, L.135, L.165, A.166, M.167, S.168, G.173, S.174, W.198, T.200, K.245, T.253, L.402, I.405, G.406, A.407, G.408, T.409, E.411, L.415 Chain D: R.312, F.315, I.319, F.322, L.324, M.325, Q.380, C.381, G.383, G.384, Y.387 17 PLIP interactions: 11 interactions with chain C, 1 interactions with chain B, 5 interactions with chain D Hydrophobic interactions: C:L.135, C:L.165, C:L.165 Hydrogen bonds: C:S.174, C:T.200, C:K.245, C:A.407, C:G.408, C:T.409, C:T.409, C:E.411, B:Q.323, D:G.384 Salt bridges: D:R.312, D:R.312 pi-Stacking: D:F.322, D:F.322 FAD.4: 33 residues within 4Å: Chain A: Q.323 Chain C: Y.308, R.312, A.314, F.315, I.319, F.322, L.324, M.325, Q.380, C.381, G.383, G.384 Chain D: L.135, L.165, A.166, M.167, S.168, G.173, S.174, W.198, I.199, T.200, T.253, L.402, I.405, G.406, A.407, G.408, T.409, E.411, V.412, L.415 19 PLIP interactions: 11 interactions with chain D, 7 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: D:L.165 Hydrogen bonds: D:S.168, D:S.168, D:S.174, D:S.174, D:S.174, D:T.200, D:I.405, D:A.407, D:G.408, D:T.409, C:Y.308, C:Q.380, C:G.383, C:G.384, A:Q.323 Salt bridges: C:R.312, C:R.312 pi-Stacking: C:F.322

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ju, K. et al., Structural Insights into Isovaleryl-Coenzyme A Dehydrogenase: Mechanisms of Substrate Specificity and Implications of Isovaleric Acidemia-Associated Mutations. Res

Release Date

2025-06-11

Peptides

Isovaleryl-CoA dehydrogenase, mitochondrial: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Isovaleryl-CoA dehydrogenase, mitochondrial

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