SMTL ID : 3hyx.2 (4 other biounits)

3-D X-Ray structure of the sulfide:quinone oxidoreductase from Aquifex aeolicus in complex with Aurachin C

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

homo-trimer

Ligands

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

SO4.1: 1 residues within 4Å: Chain A: S.401 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.401 SO4.2: 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 SO4.3: 6 residues within 4Å: Chain A: K.77, K.108, P.257, E.258, V.259 Ligands: FAD.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.258, A:V.259 Salt bridges: A:K.77 SO4.4: 4 residues within 4Å: Chain A: G.375, K.376, W.377 Ligands: LMT.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.376, A:W.377 SO4.10: 3 residues within 4Å: Chain A: K.172 Chain C: R.369, K.412 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Salt bridges: C:R.369, A:K.172 SO4.11: 2 residues within 4Å: Chain A: R.369 Chain B: K.172 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Salt bridges: A:R.369, B:K.172 SO4.12: 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 Water bridges: B:W.391 Salt bridges: B:R.394 SO4.13: 5 residues within 4Å: Chain B: K.77, K.108, P.257, E.258, V.259 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.258, B:V.259 Salt bridges: B:K.77, B:K.108 SO4.14: 4 residues within 4Å: Chain B: G.375, K.376, W.377 Ligands: LMT.17 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.376, B:W.377 SO4.20: 2 residues within 4Å: Chain B: R.369 Chain C: K.172 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B Salt bridges: C:K.172, B:R.369 SO4.21: 6 residues within 4Å: Chain C: K.77, K.108, P.257, E.258, V.259 Ligands: FAD.23 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:E.258, C:V.259 Salt bridges: C:K.77, C:K.108 SO4.22: 5 residues within 4Å: Chain C: M.374, G.375, K.376, W.377 Ligands: LMT.25 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:K.376, C:W.377 Salt bridges: C:K.376

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

FAD.5: 30 residues within 4Å: Chain A: I.8, G.9, G.10, G.11, V.12, G.13, S.34, D.35, R.36, T.42, P.43, 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: SO4.3, H2S.8 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:I.123, 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:A.78, A:A.78, A:G.106, A:V.294, A:G.314, A:K.382 Water bridges: A:G.11, A:I.348, A:K.382 FAD.15: 32 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, P.107, I.123, C.124, P.159, G.293, V.294, K.312, T.313, G.314, I.317, K.382 Ligands: AUK.16, H2S.18, PS9.19 21 PLIP interactions: 21 interactions with chain B Hydrophobic interactions: B:T.42, B:I.123, 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.14, B:K.382 FAD.23: 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, P.46, E.76, K.77, A.78, A.104, T.105, G.106, P.107, I.123, C.124, P.159, G.293, V.294, K.312, T.313, G.314, I.317, K.382 Ligands: SO4.21, AUK.24, H2S.26, PS9.27 19 PLIP interactions: 19 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:T.42, C:A.78, C:A.78, C:V.294, C:G.314 Water bridges: C:G.11, C:G.14, C:V.295, C:I.348

3 x AUK: 1-hydroxy-2-methyl-3-[(2E,6E)-3,7,11-trimethyldodeca-2,6,10-trien-1-yl]quinolin-4(1H)-one(Non-covalent)

AUK.6: 13 residues within 4Å: Chain A: M.315, E.318, I.346, F.357, K.373, W.377, F.381, F.385, E.403, V.406, L.407, L.411 Ligands: LMT.7 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:I.346, A:F.357, A:F.357, A:K.373, A:W.377, A:F.381, A:F.381, A:F.381, A:F.385, A:E.403, A:V.406, A:L.407, A:L.411 Hydrogen bonds: A:E.318 pi-Stacking: A:F.385, A:F.385 AUK.16: 12 residues within 4Å: Chain B: G.314, M.315, E.318, I.346, F.381, F.385, Y.388, F.402, E.403, L.407 Ligands: FAD.15, LMT.17 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:I.346, B:F.385, B:Y.388, B:F.402, B:E.403, B:L.407 Hydrogen bonds: B:E.318, B:E.318 pi-Stacking: B:F.385, B:F.385 AUK.24: 14 residues within 4Å: Chain C: G.314, M.315, E.318, I.346, F.357, W.377, F.381, F.385, E.403, V.406, L.407, L.411 Ligands: FAD.23, LMT.25 14 PLIP interactions: 14 interactions with chain C Hydrophobic interactions: C:I.346, C:I.346, C:F.357, C:W.377, C:F.381, C:E.403, C:V.406, C:L.407, C:L.411, C:L.411 Hydrogen bonds: C:E.318, C:E.318 pi-Stacking: C:F.385, C:F.385

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

LMT.7: 6 residues within 4Å: Chain A: K.373, W.377, V.406, F.410 Ligands: SO4.4, AUK.6 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.406, A:F.410, A:F.410 Salt bridges: A:K.373 LMT.17: 8 residues within 4Å: Chain B: K.373, M.374, W.377, F.381, V.406, F.410 Ligands: SO4.14, AUK.16 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:F.381, B:F.381, B:F.410 Hydrogen bonds: B:M.374 Salt bridges: B:K.373 LMT.25: 6 residues within 4Å: Chain C: K.373, M.374, W.377, F.410 Ligands: SO4.22, AUK.24 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:F.410, C:F.410 Hydrogen bonds: C:M.374 Salt bridges: C:K.373

3 x H2S: HYDROSULFURIC ACID(Non-covalent)

H2S.8: 3 residues within 4Å: Chain A: C.124, F.254 Ligands: FAD.5 No protein-ligand interaction detected (PLIP) H2S.18: 3 residues within 4Å: Chain B: C.124, F.254 Ligands: FAD.15 No protein-ligand interaction detected (PLIP) H2S.26: 2 residues within 4Å: Chain C: C.124 Ligands: FAD.23 No protein-ligand interaction detected (PLIP)

3 x PS9: octathiocane(Non-covalent)

PS9.9: 9 residues within 4Å: Chain A: C.156, F.157, G.158, P.159, F.194, P.311, C.347, I.348, A.349 No protein-ligand interaction detected (PLIP) PS9.19: 9 residues within 4Å: Chain B: C.156, G.158, P.159, P.311, T.313, C.347, I.348, A.349 Ligands: FAD.15 No protein-ligand interaction detected (PLIP) PS9.27: 8 residues within 4Å: Chain C: C.156, F.157, G.158, P.159, F.194, C.347, A.349 Ligands: FAD.23 No protein-ligand interaction detected (PLIP)

Links

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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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