SMTL ID : 3hyw.2 (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 Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-trimer

Ligands

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

FAD.1: 33 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, I.123, C.124, C.156, P.159, V.259, G.293, V.294, K.312, T.313, G.314, I.317, C.347, K.382 Ligands: DCQ.2, H2S.4 28 PLIP interactions: 28 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:R.36, A:T.42, A:A.78, A:A.78, A:G.106, A:V.294, A:G.314, A:K.382 Water bridges: A:G.11, A:G.14, A:R.36, A:T.42, A:V.295, A:M.315, A:I.346, A:K.382, A:K.382 FAD.11: 35 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, I.348, K.382 Ligands: DCQ.12, H2S.14, PS9.15, PS9.16 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:R.36, B:R.36, B:T.42, B:A.78, B:A.78, B:V.294, B:K.312, B:G.314, B:K.382 Water bridges: B:G.11, B:G.14, B:T.42, B:T.42, B:G.106, B:M.315, B:I.348, B:I.348, B:K.382 FAD.21: 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, P.159, V.259, G.293, V.294, K.312, T.313, G.314, I.317, K.382 Ligands: DCQ.22, H2S.24, PS9.25, SO4.28 26 PLIP interactions: 26 interactions with chain C Hydrophobic interactions: C:P.159, 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:A.78, C:A.78, C:V.294, C:K.312, C:G.314 Water bridges: C:G.11, C:G.14, C:G.106, C:T.313, C:I.346, C:K.382, C:K.382, 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: 12 residues within 4Å: Chain A: M.315, E.318, I.346, I.348, F.381, F.385, Y.388, F.402, E.403, L.407 Ligands: FAD.1, LMT.3 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:I.346, A:F.381, A:Y.388, A:F.402, A:E.403 Hydrogen bonds: A:M.315 Water bridges: A:E.318, A:E.318, A:I.346, A:I.348 pi-Stacking: A:F.385 DCQ.12: 14 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, V.406, L.407 Ligands: FAD.11, LMT.13 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:F.385, B:Y.388, B:F.402, B:E.403, B:V.406, B:V.406 Hydrogen bonds: B:M.315 Water bridges: B:I.348 pi-Stacking: B:F.385 DCQ.22: 12 residues within 4Å: Chain C: G.314, M.315, E.318, I.346, I.348, F.381, F.385, F.402, E.403, L.407 Ligands: FAD.21, LMT.23 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:M.315, C:F.385, C:F.385, C:F.402, C:E.403, C:L.407 Hydrogen bonds: C:E.318 Water bridges: C:T.313, C:I.346 pi-Stacking: C:F.385

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

LMT.3: 8 residues within 4Å: Chain A: F.357, K.373, W.377, F.381, V.406, F.410 Ligands: DCQ.2, SO4.10 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.357, A:F.381, A:F.381, A:V.406, A:F.410, A:F.410 Hydrogen bonds: A:K.373 Salt bridges: A:K.373 LMT.13: 9 residues within 4Å: Chain B: F.357, K.373, W.377, F.381, V.406, F.410, L.411 Ligands: DCQ.12, SO4.20 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:F.357, B:F.381, B:V.406, B:F.410, B:F.410, B:L.411, B:L.411 Hydrogen bonds: B:K.373 Water bridges: B:M.374 Salt bridges: B:K.373 LMT.23: 8 residues within 4Å: Chain C: K.373, W.377, F.381, V.406, F.410, L.411 Ligands: DCQ.22, SO4.29 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:F.381, C:V.406, C:F.410, C:L.411 Hydrogen bonds: C:K.373 Salt bridges: C:K.373

3 x H2S: HYDROSULFURIC ACID(Non-covalent)

H2S.4: 3 residues within 4Å: Chain A: C.124, 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.24: 3 residues within 4Å: Chain C: C.124, F.254 Ligands: FAD.21 No protein-ligand interaction detected (PLIP)

5 x PS9: octathiocane(Non-covalent)

PS9.5: 4 residues within 4Å: Chain A: C.156, F.157, G.158, P.159 No protein-ligand interaction detected (PLIP) PS9.6: 4 residues within 4Å: Chain A: G.158, C.347, I.348, A.349 No protein-ligand interaction detected (PLIP) PS9.15: 8 residues within 4Å: Chain B: C.156, F.157, G.158, P.159, P.311, T.313 Ligands: FAD.11, PS9.16 No protein-ligand interaction detected (PLIP) PS9.16: 4 residues within 4Å: Chain B: C.156, C.347 Ligands: FAD.11, PS9.15 No protein-ligand interaction detected (PLIP) PS9.25: 7 residues within 4Å: Chain C: C.156, F.157, G.158, P.159, C.347, I.348 Ligands: FAD.21 No protein-ligand interaction detected (PLIP)

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

SO4.7: 3 residues within 4Å: Chain A: R.369, K.412 Chain B: K.172 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Salt bridges: A:R.369, A:K.412, B:K.172 SO4.8: 3 residues within 4Å: Chain A: W.391, R.394, N.395 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.395 Salt bridges: A:R.394 SO4.9: 4 residues within 4Å: Chain A: K.77, K.108, P.257, E.258 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.258 Salt bridges: A:K.77, A:K.108 SO4.10: 4 residues within 4Å: Chain A: G.375, K.376, W.377 Ligands: LMT.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.376, A:W.377 SO4.17: 3 residues within 4Å: Chain B: R.369, K.412 Chain C: K.172 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain B Salt bridges: C:K.172, B:R.369, B:K.412 SO4.18: 3 residues within 4Å: Chain B: W.391, R.394, N.395 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:W.391, B:N.395 Salt bridges: B:R.394 SO4.19: 5 residues within 4Å: Chain B: K.77, K.108, P.257, E.258, V.259 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.258, B:V.259 Salt bridges: B:K.77 SO4.20: 5 residues within 4Å: Chain B: M.374, 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 SO4.26: 2 residues within 4Å: Chain A: K.172 Chain C: R.369 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C Salt bridges: A:K.172, C:R.369 SO4.27: 3 residues within 4Å: Chain C: W.391, R.394, N.395 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.395 Water bridges: C:N.395 Salt bridges: C:R.394 SO4.28: 6 residues within 4Å: Chain C: K.77, K.108, P.257, E.258, V.259 Ligands: FAD.21 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:E.258, C:V.259 Salt bridges: C:K.77 SO4.29: 4 residues within 4Å: Chain C: G.375, K.376, W.377 Ligands: LMT.23 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
B

B
D

C
F

Sulfide-quinone reductase

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