SMTL ID : 5idu.1

Crystal structure of an acyl-CoA dehydrogenase domain protein from Burkholderia phymatum bound to FAD

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-tetramer

Ligands

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

FAD.1: 30 residues within 4Å: Chain A: F.144, A.145, L.146, S.147, G.152, S.153, W.177, I.178, S.179, H.226, L.228, A.377, I.380, Y.381, A.384, E.386, V.387, L.390 Chain B: R.287, M.289, F.290, L.294, F.297, Q.355, L.356, G.358, G.359, V.362 Chain D: Q.298 Ligands: EDO.4 32 PLIP interactions: 20 interactions with chain A, 11 interactions with chain B, 1 interactions with chain D Hydrophobic interactions: A:W.177, A:L.228, A:Y.381, A:Y.381, B:V.362 Hydrogen bonds: A:F.144, A:L.146, A:S.147, A:S.147, A:G.152, A:S.153, A:S.153, A:S.179, A:E.382, B:Q.355, B:G.358, B:G.359, D:Q.298 Water bridges: A:F.144, A:S.147, A:E.148, A:G.152, A:S.179, A:G.383, B:R.283, B:R.283, B:R.287, B:M.360 pi-Stacking: A:Y.381, B:F.297 Salt bridges: B:R.287, B:R.287 FAD.5: 30 residues within 4Å: Chain A: R.287, M.289, F.290, L.294, F.297, Q.355, L.356, G.358, G.359, V.362 Chain B: F.144, A.145, L.146, S.147, G.152, S.153, W.177, I.178, S.179, H.226, L.228, A.377, I.380, Y.381, A.384, E.386, V.387, L.390 Chain C: Q.298 Ligands: EDO.8 31 PLIP interactions: 20 interactions with chain B, 10 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: B:W.177, B:L.228, B:Y.381, A:V.362 Hydrogen bonds: B:F.144, B:L.146, B:S.147, B:S.147, B:S.153, B:S.153, B:S.179, B:E.382, A:Q.355, A:G.359, C:Q.298 Water bridges: B:F.144, B:S.147, B:E.148, B:G.152, B:G.152, B:D.154, B:S.179, B:G.383, A:R.283, A:R.283, A:R.287, A:M.360 pi-Stacking: B:Y.381, A:F.297 Salt bridges: A:R.287, A:R.287 FAD.9: 27 residues within 4Å: Chain B: Q.298 Chain C: F.144, L.146, S.147, G.152, S.153, W.177, I.178, S.179, H.226, A.377, I.380, Y.381, A.384, E.386, V.387, L.390 Chain D: R.287, M.289, F.290, L.294, F.297, Q.355, L.356, G.358, G.359, V.362 26 PLIP interactions: 15 interactions with chain C, 1 interactions with chain B, 10 interactions with chain D Hydrophobic interactions: C:Y.381, D:V.362 Hydrogen bonds: C:F.144, C:L.146, C:S.147, C:S.147, C:S.153, C:S.153, C:S.179, B:Q.298, D:Q.355, D:G.359 Water bridges: C:S.147, C:E.148, C:G.152, C:D.154, C:S.179, C:E.382, D:R.283, D:R.283, D:R.287, D:M.360 pi-Stacking: C:Y.381, D:F.297 Salt bridges: D:R.287, D:R.287 FAD.13: 28 residues within 4Å: Chain A: Q.298 Chain C: R.287, M.289, F.290, L.294, F.297, Q.355, L.356, G.358, G.359, V.362 Chain D: F.144, A.145, L.146, S.147, G.152, S.153, W.177, I.178, S.179, H.226, L.228, I.380, Y.381, A.384, E.386, V.387, L.390 30 PLIP interactions: 10 interactions with chain C, 19 interactions with chain D, 1 interactions with chain A Hydrophobic interactions: C:V.362, D:W.177, D:L.228, D:Y.381, D:Y.381, D:Y.381 Hydrogen bonds: C:G.358, C:G.359, D:F.144, D:L.146, D:S.147, D:S.147, D:S.147, D:S.153, D:S.153, D:S.179, D:E.386, A:Q.298 Water bridges: C:R.283, C:R.283, C:R.287, C:M.360, D:E.148, D:G.152, D:S.179, D:E.382, D:E.382 Salt bridges: C:R.287, C:R.287 pi-Stacking: C:F.297

11 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 7 residues within 4Å: Chain A: A.20, L.93, E.96, L.270, R.274, A.315, Y.319 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.274 EDO.3: 8 residues within 4Å: Chain A: R.274, L.277, A.308, I.311, D.312 Chain D: R.333, M.337, L.396 4 PLIP interactions: 1 interactions with chain D, 3 interactions with chain A Hydrogen bonds: D:R.333, A:R.274 Water bridges: A:R.274, A:D.312 EDO.4: 3 residues within 4Å: Chain A: Y.381, E.382 Ligands: FAD.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.382 EDO.6: 6 residues within 4Å: Chain B: A.20, L.93, E.96, L.270, R.274, Y.319 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.274 EDO.7: 8 residues within 4Å: Chain B: R.274, L.277, A.308, I.311, D.312 Chain C: R.333, M.337, L.396 4 PLIP interactions: 1 interactions with chain C, 3 interactions with chain B Hydrogen bonds: C:R.333, B:R.274 Water bridges: B:R.274, B:D.312 EDO.8: 4 residues within 4Å: Chain B: L.258, Y.381, E.382 Ligands: FAD.5 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.382 EDO.10: 7 residues within 4Å: Chain C: A.20, L.93, E.96, L.270, R.274, A.315, Y.319 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.274 EDO.11: 8 residues within 4Å: Chain B: R.333, M.337, L.396 Chain C: R.274, L.277, A.308, I.311, D.312 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:R.274, B:R.333 Water bridges: C:R.274, C:D.312 EDO.12: 5 residues within 4Å: Chain C: R.95, A.110, L.114, F.261, E.382 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:R.95 Water bridges: C:R.95, C:L.258, C:F.261, C:Y.381 EDO.14: 7 residues within 4Å: Chain D: A.20, L.93, E.96, L.270, R.274, A.315, Y.319 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:R.274 EDO.15: 7 residues within 4Å: Chain A: R.333, M.337, L.396 Chain D: R.274, A.308, I.311, D.312 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:R.274, A:R.333 Water bridges: D:R.274, D:D.312

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Edwards, T.E. et al., Crystal structure of an acyl-CoA dehydrogenase domain protein from Burkholderia phymatum bound to FAD. To Be Published

Release Date

2016-03-09

Peptides

Acyl-CoA dehydrogenase domain protein: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Acyl-CoA dehydrogenase domain protein