SMTL ID : 5jsc.1 (4 other biounits)

Crystal structure of a Putative acyl-CoA dehydrogenase from Burkholderia xenovorans

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-tetramer

Ligands

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

FAD.1: 26 residues within 4Å: Chain A: F.144, L.146, S.147, G.152, S.153, W.177, I.178, S.179, L.228, 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 36 PLIP interactions: 13 interactions with chain B, 22 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: B:V.362, A:W.177, A:L.228, A:L.228, A:Y.381, A:Y.381 Hydrogen bonds: B:Q.355, B:G.358, B:G.359, 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, A:E.386, D:Q.298 Water bridges: B:R.283, B:R.283, B:R.287, B:R.287, B:K.303, B:M.360, A:F.144, A:S.147, A:G.152, A:D.154, A:S.179, A:G.383, A:G.383 Salt bridges: B:R.287, B:R.287 pi-Stacking: B:F.297 FAD.8: 26 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, L.146, S.147, G.152, S.153, W.177, I.178, S.179, L.228, I.380, Y.381, A.384, E.386, V.387, L.390 Chain C: Q.298 37 PLIP interactions: 1 interactions with chain C, 24 interactions with chain B, 12 interactions with chain A Hydrogen bonds: C:Q.298, B:F.144, B:L.146, B:S.147, B:S.147, B:G.152, B:S.153, B:S.153, B:S.179, B:E.382, B:E.386, B:E.386, A:Q.355, A:G.358, A:G.359 Hydrophobic interactions: B:W.177, B:L.228, B:L.228, B:Y.381, B:Y.381, A:V.362 Water bridges: B:F.144, B:S.147, B:G.152, B:D.154, B:W.177, B:S.179, B:G.383, B:G.383, A:R.283, A:R.283, A:R.287, A:K.303, A:M.360 Salt bridges: A:R.287, A:R.287 pi-Stacking: A:F.297 FAD.14: 26 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, L.228, 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 36 PLIP interactions: 23 interactions with chain C, 12 interactions with chain D, 1 interactions with chain B Hydrophobic interactions: C:W.177, C:L.228, C:Y.381, D:V.362 Hydrogen bonds: C:F.144, C:L.146, C:S.147, C:S.147, C:G.152, C:S.153, C:S.153, C:S.179, C:E.386, C:E.386, D:Q.355, D:G.358, D:G.359, B:Q.298 Water bridges: C:F.144, C:S.147, C:E.148, C:G.152, C:G.152, C:D.154, C:S.179, C:G.383, C:G.383, D:R.283, 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.17: 26 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, L.146, S.147, G.152, S.153, W.177, I.178, S.179, L.228, I.380, Y.381, A.384, E.386, V.387, L.390 32 PLIP interactions: 19 interactions with chain D, 12 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: D:W.177, D:L.228, D:Y.381, C:V.362 Hydrogen bonds: D:F.144, D:L.146, D:S.147, D:S.147, D:S.153, D:S.153, D:S.179, D:E.386, C:Q.355, C:G.358, C:G.359, A:Q.298 Water bridges: D:S.147, D:E.148, D:G.152, D:G.152, D:G.152, D:S.179, D:E.382, C:R.283, C:R.283, C:R.283, C:R.287, C:M.360 pi-Stacking: D:Y.381, C:F.297 Salt bridges: C:R.287, C:R.287

4 x CL: CHLORIDE ION(Non-functional Binders)

CL.2: 1 residues within 4Å: Chain A: R.29 Ligand excluded by PLIP CL.9: 2 residues within 4Å: Chain B: P.28, R.29 Ligand excluded by PLIP CL.15: 1 residues within 4Å: Chain C: R.29 Ligand excluded by PLIP CL.18: 3 residues within 4Å: Chain D: E.27, P.28, R.29 Ligand excluded by PLIP

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

EDO.3: 7 residues within 4Å: Chain A: A.20, L.93, E.96, L.270, R.274, A.315, Y.319 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.274 Water bridges: A:L.21, A:E.96, A:T.97 EDO.10: 7 residues within 4Å: Chain B: A.20, L.93, E.96, L.270, R.274, A.315, Y.319 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.274 Water bridges: B:L.21, B:E.96 EDO.16: 7 residues within 4Å: Chain C: A.20, L.93, E.96, L.270, R.274, A.315, Y.319 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:R.274 Water bridges: C:L.21, C:E.96, C:T.97 EDO.19: 7 residues within 4Å: Chain D: A.20, L.93, E.96, L.270, R.274, A.315, Y.319 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:R.274 Water bridges: D:L.21, D:E.96, D:E.96

9 x SO4: SULFATE ION(Non-functional Binders)

SO4.4: 6 residues within 4Å: Chain A: Q.306, L.309, T.310, S.313, H.341 Chain D: H.341 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain D Hydrogen bonds: A:S.313, A:S.313 Water bridges: A:Q.306, D:S.313, D:H.341 Salt bridges: A:H.341, D:H.341 SO4.5: 4 residues within 4Å: Chain A: E.27, R.29, R.89, Q.327 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:E.27, A:E.27, A:R.29, A:Q.327 Water bridges: A:R.29, A:Q.327, A:Q.327 Salt bridges: A:R.89 SO4.6: 3 residues within 4Å: Chain A: T.85, I.86, R.325 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:I.86, A:I.86 Water bridges: A:T.85, A:R.325 Salt bridges: A:R.325 SO4.7: 3 residues within 4Å: Chain A: S.102, G.103, L.104 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.103, A:L.104 Water bridges: A:H.101 SO4.11: 6 residues within 4Å: Chain B: Q.306, L.309, T.310, S.313, H.341 Chain C: H.341 9 PLIP interactions: 5 interactions with chain B, 4 interactions with chain C Hydrogen bonds: B:L.309, B:S.313 Water bridges: B:Q.306, B:H.341, C:S.313, C:S.313, C:S.313 Salt bridges: B:H.341, C:H.341 SO4.12: 3 residues within 4Å: Chain B: T.85, I.86, R.325 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:I.86, B:I.86 Water bridges: B:D.84 Salt bridges: B:R.325 SO4.13: 3 residues within 4Å: Chain B: E.27, R.89, Q.327 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.29, B:Q.327 Salt bridges: B:R.89 SO4.20: 3 residues within 4Å: Chain D: P.212, G.213, E.215 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:G.213 SO4.21: 3 residues within 4Å: Chain D: E.27, R.29, R.89 5 PLIP interactions: 5 interactions with chain D Water bridges: D:E.27, D:R.29, D:D.87 Salt bridges: D:R.29, D:R.89

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Abendroth, J. et al., Crystal structure of a Putative acyl-CoA dehydrogenase from Burkholderia xenovorans. to be published

Release Date

2016-06-08

Peptides

Putative acyl-CoA dehydrogenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

C
A

D
B

Putative acyl-CoA dehydrogenase

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