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

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 4 residues within 4Å: Chain A: W.391, R.394, N.395 Chain B: S.401 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:N.395, B:S.401 Salt bridges: A:R.394 SO4.2: 6 residues within 4Å: Chain A: K.77, K.108, P.257, E.258, V.259 Ligands: FAD.4 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.258, A:V.259 Salt bridges: A:K.77, A:K.108 SO4.3: 4 residues within 4Å: Chain A: G.375, K.376, W.377 Ligands: LMT.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.376, A:W.377 SO4.9: 1 residues within 4Å: Chain A: K.172 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.172 SO4.10: 1 residues within 4Å: Chain B: K.172 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:K.172 SO4.11: 4 residues within 4Å: Chain A: S.401 Chain B: W.391, R.394, N.395 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:N.395, A:S.401, A:S.401 Salt bridges: B:R.394 Water bridges: A:S.401 SO4.12: 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 SO4.13: 4 residues within 4Å: Chain B: G.375, K.376, W.377 Ligands: LMT.16 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.376, B:W.377 SO4.19: 1 residues within 4Å: Chain B: R.369 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.369

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

FAD.4: 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, F.45, K.77, A.78, A.104, T.105, G.106, I.123, C.124, P.159, V.259, G.293, V.294, K.312, T.313, G.314, I.317, K.382 Ligands: SO4.2, AUK.5, H2S.7, PS9.8 23 PLIP interactions: 23 interactions with chain A Hydrophobic interactions: A:F.45, A:I.123, 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:G.106, A:V.294, A:T.313, A:G.314, A:K.382 Water bridges: A:G.11, A:G.14, A:M.315 FAD.14: 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.15, H2S.17, PS9.18 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

2 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.5: 15 residues within 4Å: Chain A: G.314, M.315, E.318, I.346, F.357, K.373, F.381, F.385, E.403, L.407, F.410, L.411 Ligands: FAD.4, LMT.6, AUK.15 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:I.346, A:I.346, A:F.357, A:F.381, A:L.407, A:F.410, A:L.411 Hydrogen bonds: A:E.318 Water bridges: A:T.313 pi-Stacking: A:F.385, A:F.385 AUK.15: 17 residues within 4Å: Chain A: Y.388, F.402, E.403 Chain B: G.314, M.315, E.318, I.346, F.381, F.385, Y.388, F.402, E.403, L.407 Ligands: AUK.5, LMT.6, FAD.14, LMT.16 13 PLIP interactions: 10 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:I.346, B:F.385, B:Y.388, B:F.402, B:E.403, B:L.407, A:Y.388, A:F.402, A:E.403 Hydrogen bonds: B:E.318, B:E.318 pi-Stacking: B:F.385, B:F.385

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

LMT.6: 12 residues within 4Å: Chain A: K.373, M.374, W.377, F.410 Chain B: F.381, A.384, F.385, Y.388 Ligands: SO4.3, AUK.5, AUK.15, LMT.16 9 PLIP interactions: 6 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:F.410, A:F.410, A:F.410, B:F.381, B:A.384, B:Y.388 Hydrogen bonds: A:K.373, A:K.373, A:M.374 LMT.16: 10 residues within 4Å: Chain A: F.381 Chain B: K.373, M.374, W.377, F.381, V.406, F.410 Ligands: LMT.6, SO4.13, AUK.15 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:F.381, B:F.381, B:F.410, A:F.381 Hydrogen bonds: B:M.374 Salt bridges: B:K.373

2 x H2S: HYDROSULFURIC ACID(Non-covalent)

H2S.7: 2 residues within 4Å: Chain A: C.124 Ligands: FAD.4 No protein-ligand interaction detected (PLIP) H2S.17: 3 residues within 4Å: Chain B: C.124, F.254 Ligands: FAD.14 No protein-ligand interaction detected (PLIP)

2 x PS9: octathiocane(Non-covalent)

PS9.8: 8 residues within 4Å: Chain A: C.156, G.158, P.159, P.311, C.347, I.348, A.349 Ligands: FAD.4 No protein-ligand interaction detected (PLIP) PS9.18: 9 residues within 4Å: Chain B: C.156, G.158, P.159, P.311, T.313, C.347, I.348, A.349 Ligands: FAD.14 No protein-ligand interaction detected (PLIP)

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: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

Sulfide-quinone reductase

Related Entries With Identical Sequence