SMTL ID : 5af7.1

3-Sulfinopropionyl-coenzyme A (3SP-CoA) desulfinase from Advenella mimigardefordensis DPN7T: crystal structure and function of a desulfinase with an acyl-CoA dehydrogenase fold. Native crystal structure

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.89 Å

Oligo State

homo-tetramer

Ligands

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

FAD.1: 32 residues within 4Å: Chain A: R.84, I.121, C.122, I.123, S.124, G.129, S.130, W.154, I.155, T.156, E.210, M.361, A.365, G.366, T.368, Q.370, I.371, Q.387 Chain B: R.272, Q.274, F.275, L.279, F.282, L.285, Q.339, F.340, G.342, S.343, Y.346 Chain D: Q.283, W.287 Ligands: GOL.2 31 PLIP interactions: 13 interactions with chain B, 17 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: B:Y.346, A:W.154, A:W.154, A:A.365 Hydrogen bonds: B:Q.274, B:Q.339, B:S.343, B:S.343, B:S.343, A:I.121, A:I.123, A:S.124, A:S.124, A:S.124, A:S.130, A:S.130, A:T.156, A:G.366, A:T.368, A:Q.387, D:Q.283 Water bridges: B:R.272, B:R.272, B:R.272, B:R.272, A:Y.153, A:Y.153, A:T.156 Salt bridges: B:R.272, B:R.272 pi-Stacking: B:F.282 FAD.3: 33 residues within 4Å: Chain A: R.272, Q.274, F.275, L.279, F.282, L.285, Q.339, F.340, G.342, S.343, Y.346 Chain B: R.84, I.121, C.122, I.123, S.124, G.129, S.130, Y.153, W.154, I.155, T.156, E.210, M.361, A.365, G.366, T.368, Q.370, I.371, Q.387 Chain C: Q.283, W.287 Ligands: GOL.4 31 PLIP interactions: 22 interactions with chain B, 8 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: B:W.154, B:W.154, B:A.365, A:Y.346 Hydrogen bonds: B:R.84, B:I.121, B:I.123, B:S.124, B:S.124, B:S.124, B:S.130, B:S.130, B:Y.153, B:Y.153, B:T.156, B:T.156, B:G.366, B:T.368, B:T.368, B:Q.387, A:Q.274, A:Q.339, A:S.343, A:S.343, C:Q.283 Water bridges: B:S.124, B:G.129, B:T.374, A:S.344 Salt bridges: A:R.272, A:R.272 FAD.5: 32 residues within 4Å: Chain B: Q.283, W.287 Chain C: R.84, I.121, C.122, I.123, S.124, G.129, S.130, W.154, I.155, T.156, E.210, M.361, A.365, G.366, T.368, Q.370, I.371, Q.387 Chain D: R.272, Q.274, F.275, L.279, F.282, L.285, Q.339, F.340, G.342, S.343, Y.346 Ligands: GOL.6 31 PLIP interactions: 17 interactions with chain C, 13 interactions with chain D, 1 interactions with chain B Hydrophobic interactions: C:W.154, C:W.154, C:A.365, D:Y.346 Hydrogen bonds: C:I.121, C:I.123, C:S.124, C:S.124, C:S.124, C:S.130, C:S.130, C:T.156, C:G.366, C:T.368, C:Q.387, D:Q.274, D:Q.339, D:S.343, D:S.343, D:S.343, B:Q.283 Water bridges: C:Y.153, C:Y.153, C:T.156, D:R.272, D:R.272, D:R.272, D:R.272 Salt bridges: D:R.272, D:R.272 pi-Stacking: D:F.282 FAD.7: 33 residues within 4Å: Chain A: Q.283, W.287 Chain C: R.272, Q.274, F.275, L.279, F.282, L.285, Q.339, F.340, G.342, S.343, Y.346 Chain D: R.84, I.121, C.122, I.123, S.124, G.129, S.130, Y.153, W.154, I.155, T.156, E.210, M.361, A.365, G.366, T.368, Q.370, I.371, Q.387 Ligands: GOL.8 31 PLIP interactions: 8 interactions with chain C, 22 interactions with chain D, 1 interactions with chain A Hydrophobic interactions: C:Y.346, D:W.154, D:W.154, D:A.365 Hydrogen bonds: C:Q.274, C:Q.339, C:S.343, C:S.343, D:R.84, D:I.121, D:I.123, D:S.124, D:S.124, D:S.124, D:S.130, D:S.130, D:Y.153, D:Y.153, D:T.156, D:T.156, D:G.366, D:T.368, D:T.368, D:Q.387, A:Q.283 Water bridges: C:S.344, D:S.124, D:G.129, D:T.374 Salt bridges: C:R.272, C:R.272

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 6 residues within 4Å: Chain A: R.84, I.121, Q.246, A.365, G.366 Ligands: FAD.1 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.84 Water bridges: A:D.88, A:T.156, A:Q.246, A:Q.246, A:A.365, A:G.366 GOL.4: 7 residues within 4Å: Chain B: R.84, I.121, Y.243, Q.246, A.365, G.366 Ligands: FAD.3 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.84, B:Q.246 Water bridges: B:D.88, B:D.88, B:D.88 GOL.6: 6 residues within 4Å: Chain C: R.84, I.121, Q.246, A.365, G.366 Ligands: FAD.5 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:R.84 Water bridges: C:D.88, C:T.156, C:Q.246, C:Q.246, C:A.365, C:G.366 GOL.8: 7 residues within 4Å: Chain D: R.84, I.121, Y.243, Q.246, A.365, G.366 Ligands: FAD.7 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:R.84, D:Q.246 Water bridges: D:D.88, D:D.88, D:D.88

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schurmann, M. et al., 3-Sulfinopropionyl-Coenzyme a (3Sp-Coa) Desulfinase from Advenella Mimigardefordensis Dpn7(T): Crystal Structure and Function of a Desulfinase with an Acyl-Coa Dehydrogenase Fold. Acta Crystallogr.,Sect.D (2015)

Release Date

2015-06-03

Peptides

ACYL-COA DEHYDROGENASE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

ACYL-COA DEHYDROGENASE

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