SMTL ID : 5lvw.1

XiaF (FADH2) from Streptomyces sp.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

homo-tetramer

Ligands

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

FAD.1: 18 residues within 4Å: Chain A: W.103, N.107, S.137, V.138, F.139, A.140, Y.160, T.162, W.202, T.383, R.386, H.387, A.388 Chain D: R.282, A.285, A.365, A.366 Ligands: IND.2 13 PLIP interactions: 9 interactions with chain A, 4 interactions with chain D Hydrophobic interactions: A:W.103, A:Y.160, A:W.202, D:A.365 Hydrogen bonds: A:S.137, A:F.139, A:A.140, A:T.162, A:A.388, D:A.365, D:A.366 pi-Stacking: A:H.387 Salt bridges: D:R.282 FAD.4: 18 residues within 4Å: Chain B: W.103, N.107, S.137, V.138, F.139, A.140, Y.160, T.162, W.202, T.383, R.386, H.387, A.388 Chain C: R.282, A.285, A.365, A.366 Ligands: IND.5 13 PLIP interactions: 9 interactions with chain B, 4 interactions with chain C Hydrophobic interactions: B:W.103, B:Y.160, B:W.202, C:A.365 Hydrogen bonds: B:S.137, B:F.139, B:A.140, B:T.162, B:A.388, C:A.365, C:A.366 pi-Stacking: B:H.387 Salt bridges: C:R.282 FAD.7: 18 residues within 4Å: Chain B: R.282, A.285, A.365, A.366 Chain C: W.103, N.107, S.137, V.138, F.139, A.140, Y.160, T.162, W.202, T.383, R.386, H.387, A.388 Ligands: IND.8 15 PLIP interactions: 11 interactions with chain C, 4 interactions with chain B Hydrophobic interactions: C:W.103, C:Y.160, C:W.202, B:A.365 Hydrogen bonds: C:S.137, C:F.139, C:A.140, C:Y.160, C:T.162, C:T.162, C:A.388, B:A.365, B:A.366 pi-Stacking: C:H.387 Salt bridges: B:R.282 FAD.10: 18 residues within 4Å: Chain A: R.282, A.285, A.365, A.366 Chain D: W.103, N.107, S.137, V.138, F.139, A.140, Y.160, T.162, W.202, T.383, R.386, H.387, A.388 Ligands: IND.11 15 PLIP interactions: 11 interactions with chain D, 4 interactions with chain A Hydrophobic interactions: D:W.103, D:Y.160, D:W.202, A:A.365 Hydrogen bonds: D:S.137, D:F.139, D:A.140, D:Y.160, D:T.162, D:T.162, D:A.388, A:A.365, A:A.366 pi-Stacking: D:H.387 Salt bridges: A:R.282

4 x IND: INDOLE(Non-covalent)

IND.2: 6 residues within 4Å: Chain A: L.114, S.137, F.139, I.253, M.389 Ligands: FAD.1 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.114, A:I.253 Hydrogen bonds: A:S.137, A:S.137 pi-Stacking: A:F.139, A:F.139 IND.5: 6 residues within 4Å: Chain B: L.114, S.137, F.139, I.253, M.389 Ligands: FAD.4 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:L.114, B:I.253 Hydrogen bonds: B:S.137, B:S.137 pi-Stacking: B:F.139, B:F.139 IND.8: 6 residues within 4Å: Chain C: L.114, S.137, F.139, I.253, M.389 Ligands: FAD.7 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:L.114, C:I.253 Hydrogen bonds: C:S.137, C:S.137 pi-Stacking: C:F.139, C:F.139 IND.11: 6 residues within 4Å: Chain D: L.114, S.137, F.139, I.253, M.389 Ligands: FAD.10 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:L.114, D:I.253 Hydrogen bonds: D:S.137, D:S.137 pi-Stacking: D:F.139, D:F.139

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

SO4.3: 1 residues within 4Å: Chain A: R.120 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.120 SO4.6: 1 residues within 4Å: Chain B: R.120 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.120 SO4.9: 1 residues within 4Å: Chain C: R.120 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:R.120 SO4.12: 1 residues within 4Å: Chain D: R.120 1 PLIP interactions: 1 interactions with chain D Salt bridges: D:R.120

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kugel, S. et al., Cryptic indole hydroxylation by a non-canonical terpenoid cyclase parallels bacterial xenobiotic detoxification. Nat Commun (2017)

Release Date

2017-06-28

Peptides

XiaF protein: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

XiaF protein

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