SMTL ID : 3t2z.1

Crystal structure of sulfide:quinone oxidoreductase from Acidithiobacillus ferrooxidans

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

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

FAD.1: 38 residues within 4Å: Chain A: L.10, G.11, A.12, G.13, T.14, G.15, S.37, A.38, N.39, V.45, P.46, Q.79, S.80, A.81, A.107, T.108, G.109, P.110, I.130, C.131, C.163, P.166, V.270, A.272, G.304, I.305, K.323, T.324, G.325, I.328, V.358, F.360, K.394, M.421 Ligands: BU2.2, S3H.9, H2S.11, H2S.12 24 PLIP interactions: 24 interactions with chain A Hydrophobic interactions: A:V.45, A:P.166, A:P.166 Hydrogen bonds: A:A.12, A:A.12, A:T.14, A:T.14, A:G.15, A:G.16, A:S.37, A:A.38, A:N.39, A:A.81, A:A.81, A:I.305, A:G.325, A:F.360, A:K.394 Water bridges: A:G.13, A:T.14, A:T.14, A:V.45, A:S.80, A:G.109 FAD.15: 40 residues within 4Å: Chain B: L.10, G.11, A.12, G.13, T.14, G.15, G.16, S.37, A.38, N.39, V.45, P.46, P.49, Q.79, S.80, A.81, A.107, T.108, G.109, P.110, I.130, C.131, C.163, P.166, V.270, A.272, G.304, I.305, K.323, T.324, G.325, I.328, V.358, F.360, K.394, M.421 Ligands: BU2.14, S3H.23, H2S.24, H2S.25 25 PLIP interactions: 25 interactions with chain B Hydrophobic interactions: B:V.45, B:P.166, B:P.166 Hydrogen bonds: B:A.12, B:A.12, B:T.14, B:T.14, B:G.15, B:G.16, B:S.37, B:A.38, B:N.39, B:A.81, B:A.81, B:I.305, B:G.325, B:F.360 Water bridges: B:G.13, B:T.14, B:N.39, B:V.45, B:S.80, B:A.306, B:K.394, B:K.394

2 x BU2: 1,3-BUTANEDIOL(Non-covalent)

BU2.2: 9 residues within 4Å: Chain A: F.44, P.46, V.358, C.359, F.360, K.394, F.397, M.421 Ligands: FAD.1 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.44, A:P.46, A:F.397, A:F.397 Hydrogen bonds: A:V.358, A:F.360 Water bridges: A:A.393 BU2.14: 9 residues within 4Å: Chain B: F.44, P.46, V.358, C.359, F.360, K.394, F.397, M.421 Ligands: FAD.15 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:F.44, B:P.46 Hydrogen bonds: B:V.358, B:F.360

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

SO4.3: 5 residues within 4Å: Chain A: Y.400, R.403, K.404, K.416, K.420 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.400 Salt bridges: A:R.403, A:K.404, A:K.416, A:K.420 SO4.4: 6 residues within 4Å: Chain A: H.337, R.346, K.347, G.348, E.349, Q.350 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.349, A:Q.350 Salt bridges: A:H.337, A:R.346 SO4.5: 7 residues within 4Å: Chain A: K.404, G.408, V.409, S.410, P.412, F.413, K.416 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.400, A:S.410 Salt bridges: A:K.404, A:K.416 SO4.6: 4 residues within 4Å: Chain A: Y.198, H.201, Q.205, E.313 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.205, A:E.313, A:E.313 Salt bridges: A:H.201 SO4.7: 5 residues within 4Å: Chain A: R.66, F.76, I.77, A.78, Q.79 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.78 Salt bridges: A:R.66 SO4.16: 6 residues within 4Å: Chain B: Y.400, R.403, K.404, K.416, K.420, R.426 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Y.400 Salt bridges: B:R.403, B:K.404, B:K.416, B:K.420, B:R.426 SO4.17: 3 residues within 4Å: Chain B: D.40, R.66, A.78 2 PLIP interactions: 2 interactions with chain B Water bridges: B:A.78 Salt bridges: B:R.66 SO4.18: 6 residues within 4Å: Chain B: H.337, R.346, K.347, G.348, E.349, Q.350 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.349, B:Q.350 Salt bridges: B:H.337, B:R.346 SO4.19: 4 residues within 4Å: Chain B: Y.198, H.201, Q.205, E.313 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.205, B:E.313, B:E.313 Salt bridges: B:H.201 SO4.20: 8 residues within 4Å: Chain B: Y.400, K.404, G.408, V.409, S.410, P.412, F.413, K.416 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Y.400, B:Y.400, B:S.410 Salt bridges: B:K.404, B:K.416 SO4.21: 5 residues within 4Å: Chain B: K.179, G.182, M.183, R.184, D.185 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.182, B:R.184, B:D.185

10 x H2S: HYDROSULFURIC ACID(Non-covalent)

H2S.8: 6 residues within 4Å: Chain A: L.112, S.129, I.130, C.131, T.132, H.135 No protein-ligand interaction detected (PLIP) H2S.10: 6 residues within 4Å: Chain A: G.165, P.166, E.169, F.360, A.361 Ligands: S3H.9 No protein-ligand interaction detected (PLIP) H2S.11: 6 residues within 4Å: Chain A: T.324, C.359 Ligands: FAD.1, S3H.9, H2S.12, H2S.13 No protein-ligand interaction detected (PLIP) H2S.12: 6 residues within 4Å: Chain A: C.163, P.322 Ligands: FAD.1, S3H.9, H2S.11, H2S.13 No protein-ligand interaction detected (PLIP) H2S.13: 7 residues within 4Å: Chain A: F.164, G.165, C.359, F.370 Ligands: S3H.9, H2S.11, H2S.12 No protein-ligand interaction detected (PLIP) H2S.22: 6 residues within 4Å: Chain B: L.112, S.129, I.130, C.131, T.132, H.135 No protein-ligand interaction detected (PLIP) H2S.24: 6 residues within 4Å: Chain B: T.324, C.359 Ligands: FAD.15, S3H.23, H2S.25, H2S.26 No protein-ligand interaction detected (PLIP) H2S.25: 6 residues within 4Å: Chain B: C.163, P.322 Ligands: FAD.15, S3H.23, H2S.24, H2S.26 No protein-ligand interaction detected (PLIP) H2S.26: 6 residues within 4Å: Chain B: F.164, G.165, C.359 Ligands: S3H.23, H2S.24, H2S.25 No protein-ligand interaction detected (PLIP) H2S.27: 6 residues within 4Å: Chain B: G.165, P.166, E.169, F.360, A.361 Ligands: S3H.23 No protein-ligand interaction detected (PLIP)

2 x S3H: trisulfane(Covalent)(Non-covalent)

S3H.9: 8 residues within 4Å: Chain A: C.163, P.166, C.359 Ligands: FAD.1, H2S.10, H2S.11, H2S.12, H2S.13 No protein-ligand interaction detected (PLIP) S3H.23: 8 residues within 4Å: Chain B: C.163, P.322, C.359 Ligands: FAD.15, H2S.24, H2S.25, H2S.26, H2S.27 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cherney, M.M. et al., Crystal structure of sulfide:quinone oxidoreductase from Acidithiobacillus ferrooxidans: insights into sulfidotrophic respiration and detoxification. J.Mol.Biol. (2010)

Release Date

2011-08-17

Peptides

Sulfide-quinone reductase, putative: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Sulfide-quinone reductase, putative

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