SMTL ID : 4l1f.1 (1 other biounit)

Electron transferring flavoprotein of Acidaminococcus fermentans: Towards a mechanism of flavin-based electron bifurcation

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.79 Å

Oligo State

homo-tetramer

Ligands

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

FAD.1: 29 residues within 4Å: Chain A: F.123, L.125, T.126, G.131, T.132, F.156, I.157, T.158, T.209, I.358, I.361, Y.362, E.363, T.365, Q.367, I.371 Chain B: R.268, Q.270, F.271, I.275, F.278, L.281, Q.336, I.337, G.339, G.340, Y.341 Chain D: Q.279 Ligands: COS.2 22 PLIP interactions: 14 interactions with chain A, 2 interactions with chain D, 6 interactions with chain B Hydrophobic interactions: A:F.156, A:I.358, A:Y.362 Hydrogen bonds: A:F.123, A:L.125, A:T.126, A:T.126, A:T.132, A:T.132, A:T.158, A:E.363, A:T.365, D:Q.279, B:Q.270, B:Q.336, B:G.340 Water bridges: A:T.158, A:T.158, D:Q.279, B:R.268 Salt bridges: B:R.268, B:R.268 FAD.6: 30 residues within 4Å: Chain A: R.268, Q.270, F.271, I.275, F.278, L.281, Q.336, I.337, G.339, G.340, Y.341 Chain B: F.123, L.125, T.126, G.131, T.132, F.156, I.157, T.158, K.201, T.209, I.358, I.361, Y.362, E.363, T.365, Q.367, I.371 Chain C: Q.279 Ligands: COS.7 23 PLIP interactions: 17 interactions with chain B, 1 interactions with chain C, 5 interactions with chain A Hydrophobic interactions: B:F.156, B:K.201, B:I.358, B:Y.362 Hydrogen bonds: B:F.123, B:L.125, B:T.126, B:T.126, B:T.132, B:T.132, B:T.158, B:T.158, B:E.363, B:T.365, B:T.365, C:Q.279, A:Q.336, A:G.340 Water bridges: B:T.126, B:G.131, A:R.268 Salt bridges: A:R.268, A:R.268 FAD.10: 29 residues within 4Å: Chain B: Q.279 Chain C: F.123, L.125, T.126, G.131, T.132, F.156, I.157, T.158, T.209, I.358, I.361, Y.362, E.363, T.365, Q.367, I.371 Chain D: R.268, Q.270, F.271, I.275, F.278, L.281, Q.336, I.337, G.339, G.340, Y.341 Ligands: COS.11 22 PLIP interactions: 2 interactions with chain B, 14 interactions with chain C, 6 interactions with chain D Hydrogen bonds: B:Q.279, C:F.123, C:L.125, C:T.126, C:T.126, C:T.132, C:T.132, C:T.158, C:E.363, C:T.365, D:Q.270, D:Q.336, D:G.340 Water bridges: B:Q.279, C:T.158, C:T.158, D:R.268 Hydrophobic interactions: C:F.156, C:I.358, C:Y.362 Salt bridges: D:R.268, D:R.268 FAD.15: 30 residues within 4Å: Chain A: Q.279 Chain C: R.268, Q.270, F.271, I.275, F.278, L.281, Q.336, I.337, G.339, G.340, Y.341 Chain D: F.123, L.125, T.126, G.131, T.132, F.156, I.157, T.158, K.201, T.209, I.358, I.361, Y.362, E.363, T.365, Q.367, I.371 Ligands: COS.16 23 PLIP interactions: 17 interactions with chain D, 5 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: D:F.156, D:K.201, D:I.358, D:Y.362 Hydrogen bonds: D:F.123, D:L.125, D:T.126, D:T.126, D:T.132, D:T.132, D:T.158, D:T.158, D:E.363, D:T.365, D:T.365, C:Q.336, C:G.340, A:Q.279 Water bridges: D:T.126, D:G.131, C:R.268 Salt bridges: C:R.268, C:R.268

4 x COS: COENZYME A PERSULFIDE(Non-covalent)

COS.2: 20 residues within 4Å: Chain A: T.126, G.131, T.132, A.134, H.179, F.232, M.236, E.237, L.239, D.240, R.243, S.313, Y.362, E.363, G.364, V.368, R.375 Chain B: F.271 Ligands: FAD.1, NA.3 16 PLIP interactions: 15 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:A.134, A:V.368, B:F.271 Hydrogen bonds: A:T.132, A:A.134, A:D.240, A:R.243, A:S.313 Water bridges: A:S.135, A:E.237, A:D.240, A:D.240, A:R.243 Salt bridges: A:H.179, A:R.375, A:R.375 COS.7: 19 residues within 4Å: Chain A: F.271 Chain B: T.126, G.131, T.132, A.134, H.179, F.232, M.236, E.237, L.239, D.240, R.243, S.313, Y.362, E.363, G.364, V.368, R.375 Ligands: FAD.6 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:A.134, B:V.368 Hydrogen bonds: B:T.132, B:A.134, B:D.240, B:R.243, B:S.313 Water bridges: B:T.126, B:G.131, B:S.135, B:D.240, B:R.243 Salt bridges: B:H.179, B:R.375, B:R.375 COS.11: 20 residues within 4Å: Chain C: T.126, G.131, T.132, A.134, H.179, F.232, M.236, E.237, L.239, D.240, R.243, S.313, Y.362, E.363, G.364, V.368, R.375 Chain D: F.271 Ligands: FAD.10, NA.12 16 PLIP interactions: 15 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:A.134, C:V.368, D:F.271 Hydrogen bonds: C:T.132, C:A.134, C:D.240, C:R.243, C:S.313 Water bridges: C:S.135, C:E.237, C:D.240, C:D.240, C:R.243 Salt bridges: C:H.179, C:R.375, C:R.375 COS.16: 19 residues within 4Å: Chain C: F.271 Chain D: T.126, G.131, T.132, A.134, H.179, F.232, M.236, E.237, L.239, D.240, R.243, S.313, Y.362, E.363, G.364, V.368, R.375 Ligands: FAD.15 15 PLIP interactions: 15 interactions with chain D Hydrophobic interactions: D:A.134, D:V.368 Hydrogen bonds: D:T.132, D:A.134, D:D.240, D:R.243, D:S.313 Water bridges: D:T.126, D:G.131, D:S.135, D:D.240, D:R.243 Salt bridges: D:H.179, D:R.375, D:R.375

6 x NA: SODIUM ION(Non-functional Binders)

NA.3: 4 residues within 4Å: Chain A: L.125, T.126, G.131 Ligands: COS.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.130 NA.5: 5 residues within 4Å: Chain A: V.345, Y.347, P.348, E.350, R.351 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.347, A:R.351 NA.9: 2 residues within 4Å: Chain C: H.301, L.305 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:N.4 Water bridges: C:K.310 NA.12: 4 residues within 4Å: Chain C: L.125, T.126, G.131 Ligands: COS.11 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:G.131 NA.14: 5 residues within 4Å: Chain C: V.345, Y.347, P.348, E.350, R.351 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:V.345, C:R.351 NA.18: 2 residues within 4Å: Chain A: H.301, L.305 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.301 Water bridges: A:K.310

2 x PDO: 1,3-PROPANDIOL(Non-covalent)

PDO.4: 3 residues within 4Å: Chain A: N.4, L.5, Q.10 2 PLIP interactions: 2 interactions with chain A Water bridges: A:N.4, A:L.5 PDO.13: 3 residues within 4Å: Chain C: N.4, L.5, Q.10 2 PLIP interactions: 2 interactions with chain C Water bridges: C:N.4, C:L.5

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.8: 5 residues within 4Å: Chain B: K.291, F.322, D.325, V.326, E.329 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.329, B:E.329 Salt bridges: B:K.291 PO4.17: 5 residues within 4Å: Chain D: K.291, F.322, D.325, V.326, E.329 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:E.329, D:E.329 Salt bridges: D:K.291

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chowdhury, N.P. et al., Studies on the Mechanism of Electron Bifurcation Catalyzed by Electron Transferring Flavoprotein (Etf) and Butyryl-CoA Dehydrogenase (Bcd) of Acidaminococcus fermentans. J.Biol.Chem. (2014)

Release Date

2014-01-15

Peptides

Acyl-CoA dehydrogenase domain protein: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Acyl-CoA dehydrogenase domain protein

Related Entries With Identical Sequence