SMTL ID : 7p9x.2 (2 other biounits)

Structure of cyclohex-1-ene-1-carboxyl-CoA dehydrogenase complexed with cyclohex-1-ene-1-carboxyl-CoA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

homo-tetramer

Ligands

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

FAD.1: 32 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 Chain B: R.267, Q.269, F.270, I.274, L.277, P.279, V.280, Q.336, V.337, G.339, G.340, M.344 Ligands: 4KW.2, GOL.4 28 PLIP interactions: 20 interactions with chain A, 8 interactions with chain B Hydrophobic interactions: A:F.155, A:F.155, A:K.200, A:L.358, A:L.358, A:Y.362 Hydrogen bonds: A:L.122, A:A.124, A:T.125, A:T.125, A:S.131, A:S.131, A:T.157, A:T.157, A:T.363, A:G.364, A:T.365, A:T.365, A:Q.367, B:Q.269, B:Q.336, B:G.340 Water bridges: A:T.365, B:R.267, B:R.267, B:S.341 Salt bridges: B:R.267, B:R.267 FAD.5: 32 residues within 4Å: Chain A: R.267, Q.269, F.270, I.274, L.277, P.279, V.280, Q.336, V.337, G.339, G.340, M.344 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 Ligands: 4KW.6, GOL.8 28 PLIP interactions: 20 interactions with chain B, 8 interactions with chain A Hydrophobic interactions: B:F.155, B:F.155, B:K.200, B:L.358, 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.157, B:T.363, B:G.364, B:T.365, B:T.365, B:Q.367, A:Q.269, A:Q.336, A:G.340 Water bridges: B:T.365, A:R.267, A:R.267, A:S.341 Salt bridges: A:R.267, A:R.267 FAD.9: 32 residues within 4Å: 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 Chain D: R.267, Q.269, F.270, I.274, L.277, P.279, V.280, Q.336, V.337, G.339, G.340, M.344 Ligands: 4KW.10, GOL.12 26 PLIP interactions: 8 interactions with chain D, 18 interactions with chain C Hydrogen bonds: D:Q.269, D:Q.336, D:G.340, C:L.122, C:A.124, C:T.125, C:T.125, C:S.131, C:S.131, C:T.157, C:T.363, C:G.364, C:T.365, C:Q.367 Water bridges: D:R.267, D:R.267, D:S.341, C:T.365 Salt bridges: D:R.267, D:R.267 Hydrophobic interactions: C:F.155, C:F.155, C:K.200, C:L.358, C:L.358, C:Y.362 FAD.13: 32 residues within 4Å: Chain C: R.267, Q.269, F.270, I.274, L.277, P.279, V.280, 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 Ligands: 4KW.14, GOL.16 26 PLIP interactions: 18 interactions with chain D, 8 interactions with chain C Hydrophobic interactions: D:F.155, D:F.155, D:K.200, D:L.358, 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.363, D:G.364, D:T.365, D:Q.367, C:Q.269, C:Q.336, C:G.340 Water bridges: D:T.365, C:R.267, C:R.267, C:S.341 Salt bridges: C:R.267, C:R.267

4 x 4KW: 1-monoenoyl-CoA(Non-covalent)

4KW.2: 26 residues within 4Å: Chain A: L.84, I.87, D.91, T.125, G.130, S.131, L.133, L.134, T.157, S.177, K.178, F.231, M.235, L.238, S.239, N.241, R.242, Y.362, T.363, G.364, I.368, M.371, R.375 Chain B: F.270 Ligands: FAD.1, GOL.4 22 PLIP interactions: 21 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:L.84, A:I.87, A:L.133, A:Y.362, A:T.363, B:F.270 Hydrogen bonds: A:S.131, A:L.133, A:S.177, A:S.239, A:S.239, A:R.242, A:T.363 Water bridges: A:T.125, A:L.134, A:S.239, A:R.242, A:R.375, A:R.375 Salt bridges: A:K.178, A:R.375, A:R.375 4KW.6: 26 residues within 4Å: Chain A: F.270 Chain B: L.84, I.87, D.91, T.125, G.130, S.131, L.133, L.134, T.157, S.177, K.178, F.231, M.235, L.238, S.239, N.241, R.242, Y.362, T.363, G.364, I.368, M.371, R.375 Ligands: FAD.5, GOL.8 22 PLIP interactions: 21 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:L.84, B:I.87, B:L.133, B:Y.362, B:T.363, A:F.270 Hydrogen bonds: B:S.131, B:L.133, B:S.177, B:S.239, B:S.239, B:R.242, B:T.363 Water bridges: B:T.125, B:L.134, B:S.239, B:R.242, B:R.375, B:R.375 Salt bridges: B:K.178, B:R.375, B:R.375 4KW.10: 26 residues within 4Å: Chain C: L.84, I.87, D.91, T.125, G.130, S.131, L.133, L.134, T.157, S.177, K.178, F.231, M.235, L.238, S.239, N.241, R.242, Y.362, T.363, G.364, I.368, M.371, R.375 Chain D: F.270 Ligands: FAD.9, GOL.12 22 PLIP interactions: 21 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:L.84, C:I.87, C:L.133, C:Y.362, C:T.363, D:F.270 Hydrogen bonds: C:S.131, C:L.133, C:S.177, C:S.239, C:S.239, C:R.242, C:T.363 Water bridges: C:T.125, C:L.134, C:S.239, C:R.242, C:R.375, C:R.375 Salt bridges: C:K.178, C:R.375, C:R.375 4KW.14: 26 residues within 4Å: Chain C: F.270 Chain D: L.84, I.87, D.91, T.125, G.130, S.131, L.133, L.134, T.157, S.177, K.178, F.231, M.235, L.238, S.239, N.241, R.242, Y.362, T.363, G.364, I.368, M.371, R.375 Ligands: FAD.13, GOL.16 22 PLIP interactions: 21 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:L.84, D:I.87, D:L.133, D:Y.362, D:T.363, C:F.270 Hydrogen bonds: D:S.131, D:L.133, D:S.177, D:S.239, D:S.239, D:R.242, D:T.363 Water bridges: D:T.125, D:L.134, D:S.239, D:R.242, D:R.375, D:R.375 Salt bridges: D:K.178, D:R.375, D:R.375

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain A: D.286, M.287, A.290, R.329, V.330, D.333 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.329, A:D.333 GOL.4: 6 residues within 4Å: Chain A: M.371, R.375 Chain B: F.270, L.277 Ligands: FAD.1, 4KW.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.375 GOL.7: 6 residues within 4Å: Chain B: D.286, M.287, A.290, R.329, V.330, D.333 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.329, B:D.333 GOL.8: 6 residues within 4Å: Chain A: F.270, L.277 Chain B: M.371, R.375 Ligands: FAD.5, 4KW.6 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.375 GOL.11: 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 Water bridges: C:D.286 GOL.12: 6 residues within 4Å: Chain C: M.371, R.375 Chain D: F.270, L.277 Ligands: FAD.9, 4KW.10 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.375 GOL.15: 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 Water bridges: D:D.286 GOL.16: 6 residues within 4Å: Chain C: F.270, L.277 Chain D: M.371, R.375 Ligands: FAD.13, 4KW.14 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:R.375

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
C

B
C

C
C

D
C

Short-chain acyl-CoA dehydrogenase

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