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

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-dimer

Ligands

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

FAD.1: 25 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 35 PLIP interactions: 13 interactions with chain B, 22 interactions with chain A 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 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: 25 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 36 PLIP interactions: 24 interactions with chain B, 12 interactions with chain A Hydrophobic interactions: B:W.177, B:L.228, B:L.228, B:Y.381, B:Y.381, A:V.362 Hydrogen bonds: 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 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

2 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

2 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

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

SO4.4: 5 residues within 4Å: Chain A: Q.306, L.309, T.310, S.313, H.341 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.313, A:S.313 Water bridges: A:Q.306 Salt bridges: A: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: 5 residues within 4Å: Chain B: Q.306, L.309, T.310, S.313, H.341 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:L.309, B:S.313 Water bridges: B:Q.306 Salt bridges: B: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

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: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

Putative acyl-CoA dehydrogenase

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