SMTL ID : 7p98.1 (1 other biounit)

Cyclohex-1-ene-1-carboxyl-CoA dehydrogenase in a substrate-free state

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-tetramer

Ligands

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

FAD.1: 29 residues within 4Å: Chain A: L.122, A.124, T.125, G.130, S.131, F.155, I.156, T.157, K.200, N.208, L.358, I.361, Y.362, T.363, G.364, T.365, Q.367, I.368, M.371 Chain D: R.267, Q.269, F.270, I.274, L.277, Q.336, V.337, G.339, G.340, M.344 25 PLIP interactions: 7 interactions with chain D, 18 interactions with chain A Hydrogen bonds: D:Q.269, D:Q.336, D:G.340, A:L.122, A:A.124, A:T.125, A:T.125, A:S.131, A:S.131, A:T.157, A:T.363, A:G.364, A:T.365, A:Q.367 Water bridges: D:R.267, D:S.341, A:A.129, A:T.365 Salt bridges: D:R.267, D:R.267 Hydrophobic interactions: A:F.155, A:F.155, A:K.200, A:L.358, A:Y.362 FAD.4: 29 residues within 4Å: Chain B: L.122, A.124, T.125, G.130, S.131, F.155, I.156, T.157, K.200, N.208, L.358, I.361, Y.362, T.363, G.364, T.365, Q.367, I.368, M.371 Chain C: R.267, Q.269, F.270, I.274, L.277, Q.336, V.337, G.339, G.340, M.344 25 PLIP interactions: 18 interactions with chain B, 7 interactions with chain C Hydrophobic interactions: B:F.155, B:F.155, B:K.200, B:L.358, B:Y.362 Hydrogen bonds: B:L.122, B:A.124, B:T.125, B:T.125, B:S.131, B:S.131, B:T.157, B:T.363, B:G.364, B:T.365, B:Q.367, C:Q.269, C:Q.336, C:G.340 Water bridges: B:A.129, B:T.365, C:R.267, C:S.341 Salt bridges: C:R.267, C:R.267 FAD.7: 29 residues within 4Å: Chain B: R.267, Q.269, F.270, I.274, L.277, Q.336, V.337, G.339, G.340, M.344 Chain C: L.122, A.124, T.125, G.130, S.131, F.155, I.156, T.157, K.200, N.208, L.358, I.361, Y.362, T.363, G.364, T.365, Q.367, I.368, M.371 27 PLIP interactions: 20 interactions with chain C, 7 interactions with chain B Hydrophobic interactions: C:F.155, C:F.155, C:K.200, C:L.358, C:Y.362 Hydrogen bonds: C:L.122, C:A.124, C:T.125, C:T.125, C:S.131, C:S.131, C:T.157, C:T.157, C:T.363, C:G.364, C:T.365, C:T.365, C:Q.367, B:Q.269, B:Q.336, B:G.340 Water bridges: C:A.129, C:T.365, B:R.267, B:S.341 Salt bridges: B:R.267, B:R.267 FAD.10: 29 residues within 4Å: Chain A: R.267, Q.269, F.270, I.274, L.277, Q.336, V.337, G.339, G.340, M.344 Chain D: L.122, A.124, T.125, G.130, S.131, F.155, I.156, T.157, K.200, N.208, L.358, I.361, Y.362, T.363, G.364, T.365, Q.367, I.368, M.371 27 PLIP interactions: 20 interactions with chain D, 7 interactions with chain A Hydrophobic interactions: D:F.155, D:F.155, D:K.200, D:L.358, D:Y.362 Hydrogen bonds: D:L.122, D:A.124, D:T.125, D:T.125, D:S.131, D:S.131, D:T.157, D:T.157, D:T.363, D:G.364, D:T.365, D:T.365, D:Q.367, A:Q.269, A:Q.336, A:G.340 Water bridges: D:A.129, D:T.365, A:R.267, A:S.341 Salt bridges: A:R.267, A:R.267

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 7 residues within 4Å: Chain A: Q.254, L.257, A.288, V.291, E.292, R.295 Chain B: Y.315 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Q.254, A:A.288, A:E.292, A:R.295, A:R.295, B:Y.315 GOL.3: 6 residues within 4Å: Chain A: D.286, M.287, A.290, R.329, V.330, D.333 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.329 GOL.5: 7 residues within 4Å: Chain A: Y.315 Chain B: Q.254, L.257, A.288, V.291, E.292, R.295 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Q.254, B:A.288, B:E.292, B:R.295, B:R.295, A:Y.315 GOL.6: 6 residues within 4Å: Chain B: D.286, M.287, A.290, R.329, V.330, D.333 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.329 GOL.8: 7 residues within 4Å: Chain C: Q.254, L.257, A.288, V.291, E.292, R.295 Chain D: Y.315 6 PLIP interactions: 2 interactions with chain D, 4 interactions with chain C Hydrogen bonds: D:Y.315, D:Y.315, C:Q.254, C:A.288, C:R.295, C:R.295 GOL.9: 6 residues within 4Å: Chain C: D.286, M.287, A.290, R.329, V.330, D.333 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.329, C:D.333 GOL.11: 7 residues within 4Å: Chain C: Y.315 Chain D: Q.254, L.257, A.288, V.291, E.292, R.295 6 PLIP interactions: 4 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:Q.254, D:A.288, D:R.295, D:R.295, C:Y.315, C:Y.315 GOL.12: 6 residues within 4Å: Chain D: D.286, M.287, A.290, R.329, V.330, D.333 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.329, D:D.333

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kung, J.W. et al., Structural Basis of Cyclic 1,3-Diene Forming Acyl-Coenzyme A Dehydrogenases. Chembiochem (2021)

Release Date

2022-07-13

Peptides

Short-chain acyl-CoA dehydrogenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Short-chain acyl-CoA dehydrogenase

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