SMTL ID : 3hyw.1 (2 other biounits)

3-D X-Ray structure of the sulfide:quinone oxidoreductase of the hyperthermophilic bacterium Aquifex aeolicus in complex with decylubiquinone

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-trimer

Ligands

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

FAD.1: 35 residues within 4Å: Chain A: I.8, G.9, G.10, G.11, V.12, G.13, I.33, S.34, D.35, R.36, T.42, P.43, E.76, K.77, A.78, A.104, T.105, G.106, P.107, I.123, C.124, C.156, P.159, V.259, G.293, V.294, K.312, T.313, G.314, I.317, K.382 Ligands: DCQ.2, H2S.4, PS9.5, SO4.8 25 PLIP interactions: 25 interactions with chain A Hydrophobic interactions: A:T.42, A:P.159, A:P.159 Hydrogen bonds: A:G.10, A:G.10, A:V.12, A:G.13, A:S.34, A:D.35, A:R.36, A:R.36, A:T.42, A:T.42, A:A.78, A:A.78, A:V.294, A:G.314, A:K.382 Water bridges: A:G.11, A:G.14, A:G.106, A:G.106, A:M.315, A:I.348, A:K.382 FAD.11: 34 residues within 4Å: Chain B: I.8, G.9, G.10, G.11, V.12, G.13, I.33, S.34, D.35, R.36, T.42, P.43, E.76, K.77, A.78, A.104, T.105, G.106, I.123, C.124, C.156, P.159, V.259, G.293, V.294, K.312, T.313, G.314, I.317, K.382 Ligands: DCQ.12, H2S.14, PS9.15, SO4.17 27 PLIP interactions: 27 interactions with chain B Hydrophobic interactions: B:T.42, B:P.159, B:P.159 Hydrogen bonds: B:G.10, B:G.10, B:V.12, B:G.13, B:S.34, B:D.35, B:D.35, B:R.36, B:R.36, B:R.36, B:T.42, B:T.42, B:A.78, B:A.78, B:V.294, B:G.314, B:K.382 Water bridges: B:G.11, B:G.14, B:G.40, B:T.42, B:G.106, B:M.315, B:I.348 FAD.20: 34 residues within 4Å: Chain C: I.8, G.9, G.10, G.11, V.12, G.13, I.33, S.34, D.35, R.36, T.42, P.43, E.76, K.77, A.78, A.104, T.105, G.106, P.107, I.123, C.124, C.156, P.159, V.259, G.293, V.294, K.312, T.313, G.314, K.382 Ligands: DCQ.21, H2S.23, PS9.24, SO4.26 25 PLIP interactions: 25 interactions with chain C Hydrophobic interactions: C:T.42, C:P.159 Hydrogen bonds: C:G.10, C:G.10, C:V.12, C:G.13, C:S.34, C:D.35, C:R.36, C:R.36, C:R.36, C:T.42, C:T.42, C:A.78, C:A.78, C:V.294, C:G.314, C:K.382 Water bridges: C:G.11, C:G.14, C:G.106, C:G.106, C:M.315, C:K.382, C:K.382

3 x DCQ: 2-decyl-5,6-dimethoxy-3-methylcyclohexa-2,5-diene-1,4-dione(Non-covalent)

DCQ.2: 13 residues within 4Å: Chain A: G.314, M.315, E.318, I.346, I.348, F.381, F.385, F.402, E.403, V.406, L.407 Ligands: FAD.1, LMT.3 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:I.346, A:F.385, A:E.403, A:V.406, A:V.406, A:L.407 Water bridges: A:I.346, A:I.346, A:I.348 pi-Stacking: A:F.385 DCQ.12: 12 residues within 4Å: Chain B: G.314, M.315, E.318, I.346, I.348, F.381, F.385, Y.388, F.402, E.403, L.407 Ligands: FAD.11 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:I.346, B:F.385, B:Y.388, B:F.402 Hydrogen bonds: B:M.315 Water bridges: B:I.348 pi-Stacking: B:F.385 DCQ.21: 13 residues within 4Å: Chain C: G.314, M.315, E.318, I.346, I.348, F.381, F.385, F.402, E.403, V.406, L.407 Ligands: FAD.20, LMT.22 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:F.385, C:F.402, C:E.403, C:V.406 Water bridges: C:M.315, C:I.346, C:I.348 pi-Stacking: C:F.385

3 x LMT: DODECYL-BETA-D-MALTOSIDE(Non-covalent)

LMT.3: 7 residues within 4Å: Chain A: K.373, W.377, F.381, F.410, L.411 Ligands: DCQ.2, SO4.9 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.381, A:F.381, A:F.410, A:F.410, A:L.411, A:L.411 Hydrogen bonds: A:K.373 Salt bridges: A:K.373 LMT.13: 8 residues within 4Å: Chain B: F.357, K.373, W.377, F.381, V.406, F.410, L.411 Ligands: SO4.18 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:F.357, B:V.406, B:F.410, B:F.410, B:L.411, B:L.411 Salt bridges: B:K.373 LMT.22: 7 residues within 4Å: Chain C: K.373, W.377, F.381, F.410, L.411 Ligands: DCQ.21, SO4.27 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:F.381, C:F.381, C:F.410, C:L.411, C:L.411 Salt bridges: C:K.373

3 x H2S: HYDROSULFURIC ACID(Non-covalent)

H2S.4: 4 residues within 4Å: Chain A: C.124, M.251, F.254 Ligands: FAD.1 No protein-ligand interaction detected (PLIP) H2S.14: 3 residues within 4Å: Chain B: C.124, F.254 Ligands: FAD.11 No protein-ligand interaction detected (PLIP) H2S.23: 3 residues within 4Å: Chain C: C.124, F.254 Ligands: FAD.20 No protein-ligand interaction detected (PLIP)

3 x PS9: octathiocane(Non-covalent)

PS9.5: 8 residues within 4Å: Chain A: C.156, F.157, G.158, P.159, F.194, C.347, A.349 Ligands: FAD.1 No protein-ligand interaction detected (PLIP) PS9.15: 7 residues within 4Å: Chain B: C.156, G.158, P.159, C.347, I.348, A.349 Ligands: FAD.11 No protein-ligand interaction detected (PLIP) PS9.24: 7 residues within 4Å: Chain C: C.156, F.157, G.158, P.159, P.311, C.347 Ligands: FAD.20 No protein-ligand interaction detected (PLIP)

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

SO4.6: 3 residues within 4Å: Chain A: R.369, K.412 Chain C: K.172 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C Salt bridges: A:R.369, A:K.412, C:K.172 SO4.7: 3 residues within 4Å: Chain A: W.391, R.394, N.395 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.395, A:N.395 Salt bridges: A:R.394 SO4.8: 6 residues within 4Å: Chain A: K.77, K.108, P.257, E.258, V.259 Ligands: FAD.1 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:E.258, A:V.259 Water bridges: A:K.77, A:K.77, A:K.77, A:K.77 Salt bridges: A:K.77, A:K.108 SO4.9: 4 residues within 4Å: Chain A: G.375, K.376, W.377 Ligands: LMT.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.376, A:W.377, A:W.377 SO4.10: 2 residues within 4Å: Chain A: K.172 Chain B: R.369 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Salt bridges: B:R.369, B:K.412, A:K.172 SO4.16: 3 residues within 4Å: Chain B: W.391, R.394, N.395 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.395, B:N.395 Salt bridges: B:R.394 SO4.17: 6 residues within 4Å: Chain B: K.77, K.108, P.257, E.258, V.259 Ligands: FAD.11 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.258, B:V.259 Salt bridges: B:K.77, B:K.108 SO4.18: 4 residues within 4Å: Chain B: G.375, K.376, W.377 Ligands: LMT.13 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.376, B:W.377 SO4.19: 3 residues within 4Å: Chain B: K.172 Chain C: R.369, K.412 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain C Salt bridges: B:K.172, C:R.369, C:K.412 SO4.25: 3 residues within 4Å: Chain C: W.391, R.394, N.395 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:N.395, C:N.395 Water bridges: C:W.391 Salt bridges: C:R.394 SO4.26: 6 residues within 4Å: Chain C: K.77, K.108, P.257, E.258, V.259 Ligands: FAD.20 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:E.258, C:V.259 Water bridges: C:K.77, C:K.77 Salt bridges: C:K.77, C:K.108 SO4.27: 4 residues within 4Å: Chain C: G.375, K.376, W.377 Ligands: LMT.22 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.376, C:W.377

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Marcia, M. et al., The structure of Aquifex aeolicus sulfide:quinone oxidoreductase, a basis to understand sulfide detoxification and respiration. Proc.Natl.Acad.Sci.USA (2009)

Release Date

2009-07-14

Peptides

Sulfide-quinone reductase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
E

Sulfide-quinone reductase

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