SMTL ID : 6es9.1

Methylsuccinyl-CoA dehydrogenase of Paracoccus denitrificans with bound flavin adenine dinucleotide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.37 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 5 residues within 4Å: Chain A: E.289, P.290, N.291, R.300, N.315 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.291, A:N.291 Water bridges: A:N.315, A:N.315, A:N.315 Salt bridges: A:R.300 SO4.2: 2 residues within 4Å: Chain A: S.28, R.32 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.32 SO4.5: 5 residues within 4Å: Chain B: E.289, P.290, N.291, R.300, N.315 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:N.291, B:N.291 Water bridges: B:E.289, B:E.289, B:E.289, B:N.315 Salt bridges: B:R.300 SO4.6: 1 residues within 4Å: Chain B: S.28 No protein-ligand interaction detected (PLIP)

2 x COA: COENZYME A(Non-covalent)

COA.3: 4 residues within 4Å: Chain A: Q.74, R.81, F.473, W.476 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Q.74, A:R.81, A:R.81 Water bridges: A:Q.74 pi-Stacking: A:W.476 pi-Cation interactions: A:R.81 COA.7: 4 residues within 4Å: Chain B: Q.74, R.81, F.473, W.476 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:Q.74, B:R.81, B:R.81 Water bridges: B:Q.74, B:R.81 pi-Stacking: B:W.476, B:W.476 pi-Cation interactions: B:R.81

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

FAD.4: 28 residues within 4Å: Chain A: Q.56, T.284, A.285, F.287, T.288, G.293, S.294, W.318, I.319, T.320, R.376, E.380, I.533, F.534, A.537, E.539, I.540 Chain B: R.440, Q.442, F.443, L.447, F.450, V.453, Q.508, I.509, G.511, G.512, F.515 25 PLIP interactions: 7 interactions with chain B, 18 interactions with chain A Hydrophobic interactions: B:F.515, A:W.318, A:W.318, A:E.380, A:F.534 Hydrogen bonds: B:G.511, B:G.512, A:Q.56, A:A.285, A:F.287, A:T.288, A:T.288, A:S.294, A:S.294, A:T.320, A:F.534, A:E.539 Water bridges: B:R.440, B:N.513, A:T.288, A:T.292, A:G.293, A:A.537 Salt bridges: B:R.440, B:R.440 FAD.8: 28 residues within 4Å: Chain A: R.440, Q.442, F.443, L.447, F.450, V.453, Q.508, I.509, G.511, G.512, F.515 Chain B: Q.56, T.284, A.285, F.287, T.288, G.293, S.294, W.318, I.319, T.320, R.376, E.380, I.533, F.534, A.537, E.539, I.540 28 PLIP interactions: 21 interactions with chain B, 7 interactions with chain A Hydrophobic interactions: B:W.318, B:W.318, B:E.380, B:F.534, A:F.515 Hydrogen bonds: B:Q.56, B:A.285, B:F.287, B:T.288, B:T.288, B:S.294, B:S.294, B:T.320, B:T.320, B:F.534, B:E.539, A:G.511, A:G.512 Water bridges: B:T.284, B:A.285, B:T.288, B:T.292, B:G.293, B:A.537, A:R.440, A:N.513 Salt bridges: A:R.440, A:R.440

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schwander, T. et al., Structural basis for substrate specificity of methylsuccinyl-CoA dehydrogenase, an unusual member of the acyl-CoA dehydrogenase family. J. Biol. Chem. (2018)

Release Date

2018-01-03

Peptides

Acyl-CoA dehydrogenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Acyl-CoA dehydrogenase