SMTL ID : 3hyv.1 (4 other biounits)

3-D X-Ray structure of the sulfide:quinone oxidoreductase from the hyperthermophilic bacterium Aquifex aeolicus

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-trimer

Ligands

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

FAD.1: 32 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, K.77, A.78, A.104, T.105, G.106, P.107, I.123, C.156, P.159, V.259, G.293, V.294, K.312, T.313, G.314, I.317, K.382 Ligands: H2S.3, PS9.4, SO4.8 22 PLIP interactions: 22 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:T.42, A:T.42, A:A.78, A:A.78, A:V.294, A:K.312, A:G.314 Water bridges: A:G.11, A:G.14, A:G.106, A:K.382, A:K.382 FAD.10: 29 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, K.77, A.78, A.104, T.105, G.106, I.123, P.159, G.293, V.294, K.312, T.313, G.314, I.317, C.347, K.382 Ligands: H2S.12, SO4.17 21 PLIP interactions: 21 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: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.106 FAD.19: 31 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, K.77, A.78, A.104, T.105, G.106, P.107, I.123, P.159, V.259, G.293, V.294, K.312, T.313, G.314, I.317, K.382 Ligands: H2S.21, PS9.22, SO4.25 23 PLIP interactions: 23 interactions with chain C Hydrophobic interactions: C:T.42, 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:T.42, C:A.78, C:A.78, C:G.106, C:V.294, C:K.312, C:G.314, C:K.382 Water bridges: C:G.11, C:G.14, C:V.295

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

LMT.2: 6 residues within 4Å: Chain A: K.373, W.377, F.381, V.406, L.407 Ligands: SO4.9 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.381, A:V.406, A:L.407 Salt bridges: A:K.373 LMT.11: 7 residues within 4Å: Chain B: F.357, K.373, W.377, F.381, V.406, L.407 Ligands: SO4.18 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:F.357, B:L.407 Salt bridges: B:K.373 LMT.20: 8 residues within 4Å: Chain C: F.357, K.373, W.377, F.381, V.406, L.407, L.411 Ligands: SO4.26 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:F.357, C:V.406, C:L.407, C:L.411 Salt bridges: C:K.373

3 x H2S: HYDROSULFURIC ACID(Non-covalent)

H2S.3: 2 residues within 4Å: Chain A: C.124 Ligands: FAD.1 No protein-ligand interaction detected (PLIP) H2S.12: 2 residues within 4Å: Chain B: C.124 Ligands: FAD.10 No protein-ligand interaction detected (PLIP) H2S.21: 2 residues within 4Å: Chain C: C.124 Ligands: FAD.19 No protein-ligand interaction detected (PLIP)

3 x PS9: octathiocane(Non-covalent)

PS9.4: 7 residues within 4Å: Chain A: C.156, F.157, G.158, P.159, C.347, I.348 Ligands: FAD.1 No protein-ligand interaction detected (PLIP) PS9.13: 6 residues within 4Å: Chain B: C.156, G.158, P.159, C.347, I.348, A.349 No protein-ligand interaction detected (PLIP) PS9.22: 7 residues within 4Å: Chain C: C.156, F.157, G.158, P.159, F.194, C.347 Ligands: FAD.19 No protein-ligand interaction detected (PLIP)

3 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.5: 8 residues within 4Å: Chain A: H.168, Y.169, K.172, R.213, E.353, D.354, K.376 Ligands: SO4.15 7 PLIP interactions: 7 interactions with chain A Water bridges: A:R.213 Salt bridges: A:H.168, A:K.172, A:K.173, A:R.213, A:E.353, A:D.354 MES.14: 8 residues within 4Å: Chain B: H.168, Y.169, K.172, R.213, E.353, D.354, K.376 Ligands: SO4.28 6 PLIP interactions: 6 interactions with chain B Water bridges: B:R.213 Salt bridges: B:H.168, B:K.172, B:R.213, B:E.353, B:D.354 MES.23: 8 residues within 4Å: Chain C: H.168, Y.169, K.172, R.213, E.353, D.354, K.376 Ligands: SO4.6 4 PLIP interactions: 4 interactions with chain C Salt bridges: C:H.168, C:K.172, C:R.213, C:D.354

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

SO4.6: 4 residues within 4Å: Chain A: R.369, K.412 Chain C: K.172 Ligands: MES.23 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 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: 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 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.258, A:V.259 Salt bridges: A:K.77, A:K.108 SO4.9: 4 residues within 4Å: Chain A: G.375, K.376, W.377 Ligands: LMT.2 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.376, A:W.377, A:W.377 Salt bridges: A:K.376 SO4.15: 3 residues within 4Å: Chain A: K.172 Chain B: R.369 Ligands: MES.5 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Salt bridges: A:K.172, B:R.369 SO4.16: 3 residues within 4Å: Chain B: W.391, R.394, N.395 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: 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.10 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:E.258, B:V.259 Water bridges: B:K.77 Salt bridges: B:K.77, B:K.108 SO4.18: 4 residues within 4Å: Chain B: G.375, K.376, W.377 Ligands: LMT.11 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.376, B:W.377 SO4.24: 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, C:N.395 Salt bridges: C:R.394 SO4.25: 6 residues within 4Å: Chain C: K.77, K.108, P.257, E.258, V.259 Ligands: FAD.19 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:E.258, C:V.259 Salt bridges: C:K.77, C:K.108 SO4.26: 4 residues within 4Å: Chain C: G.375, K.376, W.377 Ligands: LMT.20 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:K.376, C:W.377, C:W.377 Salt bridges: C:K.376 SO4.27: 1 residues within 4Å: Chain C: S.401 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.401, C:S.401 SO4.28: 4 residues within 4Å: Chain B: K.172 Chain C: R.369, K.412 Ligands: MES.14 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B Salt bridges: C:R.369, C:K.412, B:K.172

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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