SMTL ID : 5lnx.1 (1 other biounit)

Crystal structure of MmgC, an acyl-CoA dehydrogenase from bacillus subtilis.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-tetramer

Ligands

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 8 residues within 4Å: Chain A: S.130, M.234, L.237, R.241, E.361, G.362, I.366 Ligands: FAD.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.241, A:E.361 GOL.2: 3 residues within 4Å: Chain A: K.42, K.45, H.46 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.42 GOL.3: 5 residues within 4Å: Chain A: F.99, G.224, D.228, H.231, I.232 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.228, A:H.231 GOL.6: 4 residues within 4Å: Chain B: H.299 Chain C: H.295, Y.298, H.299 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:H.295, C:Y.298, B:H.299 GOL.7: 5 residues within 4Å: Chain C: L.97, Y.98, F.99, G.100, K.105 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.105 GOL.8: 5 residues within 4Å: Chain B: R.289, F.320 Chain C: R.289, F.320, K.327 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.327 GOL.10: 6 residues within 4Å: Chain A: R.289 Chain D: R.289, Q.319, F.320, D.323, R.368 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:R.289, D:F.320, D:R.368, A:R.289

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

FAD.4: 28 residues within 4Å: Chain A: F.121, L.123, T.124, G.129, S.130, F.154, T.156, T.207, I.359, Y.360, E.361, T.363, E.365, I.366, L.369 Chain B: R.266, Q.268, F.269, I.273, N.276, I.279, Q.334, I.335, G.337, G.338, Y.339 Chain D: Q.277 Ligands: GOL.1 21 PLIP interactions: 15 interactions with chain A, 5 interactions with chain B, 1 interactions with chain D Hydrophobic interactions: A:F.154, A:T.207, A:Y.360 Hydrogen bonds: A:F.121, A:L.123, A:T.124, A:T.124, A:T.124, A:G.129, A:T.156, A:T.156, A:E.361, A:T.363, A:E.365, B:N.276, B:Q.334, B:G.338, D:Q.277 pi-Stacking: A:Y.360 Salt bridges: B:R.266, B:R.266 FAD.5: 29 residues within 4Å: Chain A: R.266, Q.268, F.269, R.271, I.273, N.276, I.279, Q.334, I.335, G.337, G.338, Y.339 Chain B: F.121, A.122, L.123, T.124, G.129, S.130, F.154, I.155, T.156, L.202, V.356, I.359, Y.360, E.361, T.363, E.365 Chain C: Q.277 24 PLIP interactions: 16 interactions with chain B, 7 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: B:F.154, B:L.202, B:Y.360, B:Y.360 Hydrogen bonds: B:F.121, B:T.124, B:T.124, B:T.124, B:S.130, B:S.130, B:T.156, B:T.156, B:E.361, B:T.363, B:T.363, A:R.271, A:N.276, A:Q.334, A:G.338, A:Y.339, C:Q.277 Water bridges: B:G.129 Salt bridges: A:R.266, A:R.266 FAD.9: 24 residues within 4Å: Chain B: Q.277 Chain C: F.121, L.123, T.124, G.129, S.130, F.154, T.156, T.207, Y.360, T.363, E.365, L.369 Chain D: R.266, Q.268, F.269, I.273, N.276, I.279, Q.334, I.335, G.337, G.338, Y.339 23 PLIP interactions: 7 interactions with chain D, 15 interactions with chain C, 1 interactions with chain B Hydrogen bonds: D:Q.268, D:N.276, D:Q.334, D:G.338, D:Y.339, C:F.121, C:L.123, C:T.124, C:T.124, C:T.124, C:S.130, C:S.130, C:T.156, C:E.361, C:T.363, C:E.365, B:Q.277 Salt bridges: D:R.266, D:R.266 Hydrophobic interactions: C:F.154, C:T.207, C:Y.360 pi-Stacking: C:Y.360 FAD.11: 26 residues within 4Å: Chain A: Q.277 Chain C: R.266, Q.268, F.269, R.271, I.273, N.276, I.279, Q.334, I.335, G.337, G.338, Y.339, Y.341 Chain D: F.121, L.123, T.124, G.129, S.130, F.154, T.156, L.202, V.356, Y.360, T.363, E.365 26 PLIP interactions: 15 interactions with chain D, 1 interactions with chain A, 10 interactions with chain C Hydrophobic interactions: D:F.154, D:L.202, D:V.356, D:Y.360, D:Y.360, C:Y.341 Hydrogen bonds: D:L.123, D:T.124, D:T.124, D:T.124, D:S.130, D:S.130, D:T.156, D:E.361, D:T.363, D:E.365, A:Q.277, C:R.271, C:N.276, C:N.276, C:Q.334, C:Q.334, C:G.338, C:Y.339 Salt bridges: C:R.266, C:R.266

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Baker, G.E. et al., Crystal structure of acyl-CoA dehydrogenase (MmgC) from bacillus subtilis. To Be Published

Release Date

2017-08-16

Peptides

Acyl-CoA dehydrogenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Acyl-CoA dehydrogenase

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