SMTL ID : 1buc.1

THREE-DIMENSIONAL STRUCTURE OF BUTYRYL-COA DEHYDROGENASE FROM MEGASPHAERA ELSDENII

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-tetramer

Ligands

4 x CAA: ACETOACETYL-COENZYME A(Non-covalent)

CAA.1: 22 residues within 4Å: Chain A: L.96, F.126, T.129, G.134, T.135, A.137, S.138, T.162, N.182, H.183, F.236, M.240, M.241, L.243, D.244, R.247, T.317, Y.366, E.367, G.368, V.372 Ligands: FAD.2 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:E.367 Hydrogen bonds: A:G.134, A:T.135, A:A.137, A:S.138, A:N.182, A:D.244, A:R.247, A:E.367 Salt bridges: A:H.183 CAA.3: 21 residues within 4Å: Chain B: A.92, L.96, F.126, T.129, G.134, T.135, A.137, T.162, N.182, H.183, F.236, M.240, M.241, L.243, D.244, R.247, Y.366, E.367, G.368 Chain D: F.275 Ligands: FAD.4 14 PLIP interactions: 13 interactions with chain B, 1 interactions with chain D Hydrophobic interactions: B:A.92, B:E.367, D:F.275 Hydrogen bonds: B:G.134, B:T.135, B:A.137, B:T.162, B:N.182, B:D.244, B:R.247, B:E.367, B:E.367, B:G.368 Salt bridges: B:H.183 CAA.5: 22 residues within 4Å: Chain C: L.96, F.126, T.129, G.134, T.135, A.137, S.138, T.162, N.182, H.183, F.236, M.240, M.241, L.243, D.244, R.247, T.317, Y.366, E.367, G.368, V.372 Ligands: FAD.6 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:E.367 Hydrogen bonds: C:G.134, C:T.135, C:A.137, C:S.138, C:N.182, C:D.244, C:R.247, C:E.367 Salt bridges: C:H.183 CAA.7: 21 residues within 4Å: Chain B: F.275 Chain D: A.92, L.96, F.126, T.129, G.134, T.135, A.137, T.162, N.182, H.183, F.236, M.240, M.241, L.243, D.244, R.247, Y.366, E.367, G.368 Ligands: FAD.8 14 PLIP interactions: 1 interactions with chain B, 13 interactions with chain D Hydrophobic interactions: B:F.275, D:A.92, D:E.367 Hydrogen bonds: D:G.134, D:T.135, D:A.137, D:T.162, D:N.182, D:D.244, D:R.247, D:E.367, D:E.367, D:G.368 Salt bridges: D:H.183

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

FAD.2: 31 residues within 4Å: Chain A: F.126, L.128, T.129, G.134, T.135, F.160, I.161, T.162, K.205, T.213, I.362, I.365, Y.366, E.367, T.369, E.371, M.375 Chain B: Q.283 Chain C: R.272, Q.274, F.275, L.279, F.282, S.284, I.285, Q.340, I.341, G.343, G.344, Y.345 Ligands: CAA.1 23 PLIP interactions: 16 interactions with chain A, 6 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: A:F.160, A:K.205, A:T.213, A:I.362 Hydrogen bonds: A:F.126, A:L.128, A:T.129, A:T.129, A:T.135, A:T.135, A:T.162, A:T.162, A:E.367, A:T.369, A:T.369, C:S.284, C:Q.340, C:Q.340, C:G.344, B:Q.283 pi-Stacking: A:Y.366 Salt bridges: C:R.272, C:R.272 FAD.4: 32 residues within 4Å: Chain A: Q.283 Chain B: F.126, L.128, T.129, G.134, T.135, F.160, I.161, T.162, K.205, T.213, I.362, I.365, Y.366, E.367, G.368, T.369, E.371, M.375 Chain D: R.272, Q.274, F.275, L.279, F.282, S.284, I.285, Q.340, I.341, G.343, G.344, Y.345 Ligands: CAA.3 22 PLIP interactions: 16 interactions with chain B, 5 interactions with chain D, 1 interactions with chain A Hydrophobic interactions: B:F.160, B:K.205, B:I.362, B:Y.366, B:Y.366 Hydrogen bonds: B:F.126, B:L.128, B:T.129, B:T.129, B:T.135, B:T.135, B:T.162, B:E.367, B:G.368, B:T.369, B:E.371, D:S.284, D:Q.340, D:G.344, A:Q.283 Salt bridges: D:R.272, D:R.272 FAD.6: 31 residues within 4Å: Chain A: R.272, Q.274, F.275, L.279, F.282, S.284, I.285, Q.340, I.341, G.343, G.344, Y.345 Chain C: F.126, L.128, T.129, G.134, T.135, F.160, I.161, T.162, K.205, T.213, I.362, I.365, Y.366, E.367, T.369, E.371, M.375 Chain D: Q.283 Ligands: CAA.5 23 PLIP interactions: 16 interactions with chain C, 6 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: C:F.160, C:K.205, C:T.213, C:I.362 Hydrogen bonds: C:F.126, C:L.128, C:T.129, C:T.129, C:T.135, C:T.135, C:T.162, C:T.162, C:E.367, C:T.369, C:T.369, A:S.284, A:Q.340, A:Q.340, A:G.344, D:Q.283 pi-Stacking: C:Y.366 Salt bridges: A:R.272, A:R.272 FAD.8: 32 residues within 4Å: Chain B: R.272, Q.274, F.275, L.279, F.282, S.284, I.285, Q.340, I.341, G.343, G.344, Y.345 Chain C: Q.283 Chain D: F.126, L.128, T.129, G.134, T.135, F.160, I.161, T.162, K.205, T.213, I.362, I.365, Y.366, E.367, G.368, T.369, E.371, M.375 Ligands: CAA.7 22 PLIP interactions: 16 interactions with chain D, 5 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: D:F.160, D:K.205, D:I.362, D:Y.366, D:Y.366 Hydrogen bonds: D:F.126, D:L.128, D:T.129, D:T.129, D:T.135, D:T.135, D:T.162, D:E.367, D:G.368, D:T.369, D:E.371, B:S.284, B:Q.340, B:G.344, C:Q.283 Salt bridges: B:R.272, B:R.272

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Djordjevic, S. et al., Three-dimensional structure of butyryl-CoA dehydrogenase from Megasphaera elsdenii. Biochemistry (1995)

Release Date

1995-04-20

Peptides

BUTYRYL-COA DEHYDROGENASE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

BUTYRYL-COA DEHYDROGENASE