SMTL ID : 9jq4.1

Structure of human IVD in complex with FAD and butyryl-CoA

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

4 x BCO: Butyryl Coenzyme A(Non-covalent)(Covalent)

BCO.1: 28 residues within 4Å: Chain A: L.127, A.131, L.135, L.165, M.167, S.168, G.173, S.174, D.175, V.176, V.177, T.200, S.222, R.223, Y.277, M.280, S.281, L.283, D.284, R.287, L.290, A.407, G.408, V.412, V.416, R.419 Chain B: F.315 Ligands: FAD.2 18 PLIP interactions: 17 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:L.127, A:A.131, A:L.135, A:L.283, A:L.290, A:A.407, A:V.412, A:V.416, B:F.315 Hydrogen bonds: A:G.173, A:S.174, A:D.175, A:V.176, A:S.222, A:M.280, A:R.287, A:R.419 Salt bridges: A:R.223 BCO.3: 27 residues within 4Å: Chain A: F.315 Chain B: L.127, L.135, M.167, S.168, G.173, S.174, V.176, V.177, S.222, R.223, V.276, Y.277, M.280, S.281, L.283, D.284, R.287, L.290, A.357, G.406, A.407, G.408, V.412, V.416, R.419 Ligands: FAD.4 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:L.127, B:L.135, B:L.283, B:L.290, B:A.407, B:V.416 Hydrogen bonds: B:S.168, B:S.222, B:D.284, B:R.419 Salt bridges: B:R.223, B:R.419 BCO.5: 27 residues within 4Å: Chain C: L.127, A.131, L.135, M.167, S.168, G.173, S.174, D.175, V.176, V.177, T.200, S.222, V.276, Y.277, M.280, S.281, L.283, D.284, R.287, L.290, A.407, G.408, V.412, V.416, R.419 Chain D: F.315 Ligands: FAD.6 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:L.127, C:A.131, C:L.135, C:V.176, C:A.407, C:V.412, C:V.416 Hydrogen bonds: C:S.222, C:M.280, C:R.287, C:A.407, C:A.407, C:R.419 BCO.7: 27 residues within 4Å: Chain C: F.315 Chain D: L.135, Q.139, L.165, M.167, S.168, G.173, S.174, D.175, V.176, V.177, Y.211, S.222, V.276, Y.277, L.279, M.280, G.282, L.283, D.284, R.287, A.357, A.407, G.408, V.412, R.419 Ligands: FAD.8 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:L.165, D:V.176, D:L.283, D:V.412 Hydrogen bonds: D:S.168, D:S.222, D:D.284 Salt bridges: D:R.419

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

FAD.2: 35 residues within 4Å: Chain A: L.127, A.131, L.135, L.165, M.167, S.168, G.173, S.174, W.198, I.199, T.200, K.245, L.402, I.405, G.406, A.407, G.408, T.409, E.411, V.412, L.415 Chain B: R.312, F.315, I.319, F.322, L.324, M.325, Q.380, C.381, F.382, G.383, G.384, Y.387 Chain D: Q.323 Ligands: BCO.1 16 PLIP interactions: 11 interactions with chain A, 4 interactions with chain B, 1 interactions with chain D Hydrophobic interactions: A:L.135, A:W.198 Hydrogen bonds: A:S.168, A:G.173, A:G.173, A:S.174, A:W.198, A:I.405, A:G.408, A:E.411, A:E.411, B:G.384, D:Q.323 Salt bridges: B:R.312, B:R.312 pi-Stacking: B:F.322 FAD.4: 35 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, L.402, I.405, G.406, A.407, G.408, T.409, E.411, V.412, L.415 Chain C: Q.323 Ligands: BCO.3 17 PLIP interactions: 11 interactions with chain B, 5 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: B:L.135, B:L.165, B:M.167, B:W.198 Hydrogen bonds: B:S.168, B:S.174, 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, A:F.322 FAD.6: 34 residues within 4Å: Chain B: Q.323 Chain C: L.127, L.135, L.165, A.166, M.167, S.168, G.173, S.174, W.198, T.200, L.402, I.405, G.406, A.407, G.408, T.409, E.411, V.412, L.415 Chain D: 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 Ligands: BCO.5 14 PLIP interactions: 1 interactions with chain B, 8 interactions with chain C, 5 interactions with chain D Hydrogen bonds: B:Q.323, C:S.168, C:G.173, C:S.174, C:A.407, C:G.408, D:R.312, D:Q.380, D:G.384 Hydrophobic interactions: C:L.135, C:M.167, C:W.198 Salt bridges: D:R.312 pi-Stacking: D:F.322 FAD.8: 34 residues within 4Å: Chain A: Q.323 Chain C: 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: L.127, L.135, L.165, A.166, M.167, S.168, E.169, G.173, S.174, W.198, T.200, K.245, T.253, L.402, I.405, G.406, A.407, G.408, T.409, L.415 Ligands: BCO.7 14 PLIP interactions: 9 interactions with chain D, 5 interactions with chain C Hydrophobic interactions: D:L.135, D:L.165 Hydrogen bonds: D:S.168, D:S.168, D:G.173, D:S.174, D:T.200, D:T.409, D:T.409, C:Q.380, C:G.384 Salt bridges: C:R.312 pi-Stacking: C:F.322, 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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