SMTL ID : 3szf.1

Crystal structure of sulfide:quinone oxidoreductase H198A variant from Acidithiobacillus ferrooxidans in complex with bound trisulfide and decylubiquinone

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

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

FAD.1: 39 residues within 4Å: Chain A: L.10, G.11, A.12, G.13, T.14, G.15, G.16, I.36, 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, C.359, F.360 Ligands: DCQ.3, H2S.4, S3H.5, H2S.7 26 PLIP interactions: 26 interactions with chain A Hydrophobic interactions: A:V.45, A:I.130, 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:A.81, A:A.81, A:I.305, A:G.325, A:F.360 Water bridges: A:G.13, A:T.14, A:N.39, A:N.39, A:N.39, A:N.39, A:S.80, A:G.109, A:A.306, A:K.394 FAD.10: 39 residues within 4Å: Chain B: L.10, G.11, A.12, G.13, T.14, G.15, G.16, I.36, 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, C.359, F.360 Ligands: DCQ.12, H2S.13, S3H.14, H2S.16 26 PLIP interactions: 26 interactions with chain B Hydrophobic interactions: B:V.45, B:I.130, 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: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:N.39, B:N.39, B:N.39, B:S.80, B:G.109, B:A.306, B:K.394

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

LMT.2: 17 residues within 4Å: Chain A: G.165, Y.168, M.172, I.213, L.214, G.217, E.220, C.359, F.360, A.361, A.368, A.369, F.370, F.384, Y.386 Chain B: G.208, D.209 14 PLIP interactions: 10 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:I.213, A:L.214, A:A.361, A:F.370, A:F.384, A:Y.386 Hydrogen bonds: A:E.220, A:Y.386 Water bridges: A:Y.386, A:Y.386, B:G.208, B:D.209, B:D.209, B:D.382 LMT.11: 17 residues within 4Å: Chain A: G.208, D.209 Chain B: G.165, Y.168, M.172, I.213, L.214, G.217, E.220, C.359, F.360, A.361, A.368, A.369, F.370, F.384, Y.386 16 PLIP interactions: 11 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:I.213, B:L.214, B:A.361, B:F.370, B:F.384, B:Y.386 Hydrogen bonds: B:E.220, B:Y.386 Water bridges: B:Y.386, B:Y.386, B:Y.386, A:G.208, A:D.209, A:D.209, A:D.209, A:D.382

2 x DCQ: 2-DECYL-5,6-DIMETHOXY-3-METHYLCYCLOHEXA-2,5-DIENE-1,4-DIONE(Non-covalent)

DCQ.3: 10 residues within 4Å: Chain A: F.44, P.46, G.325, Y.326, V.358, F.360, F.397, Y.414 Chain B: K.420 Ligands: FAD.1 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:Y.326, A:V.358, A:F.360, A:F.397, A:Y.414, B:K.420 DCQ.12: 10 residues within 4Å: Chain A: K.420 Chain B: F.44, P.46, G.325, Y.326, V.358, F.360, F.397, Y.414 Ligands: FAD.10 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:Y.326, B:V.358, B:F.360, B:F.397, B:Y.414, A:K.420 Hydrogen bonds: B:Y.414

8 x H2S: HYDROSULFURIC ACID(Non-covalent)(Non-functional Binders)

H2S.4: 6 residues within 4Å: Chain A: T.324, V.358, C.359 Ligands: FAD.1, S3H.5, H2S.7 No protein-ligand interaction detected (PLIP) H2S.6: 4 residues within 4Å: Chain A: F.164, G.165, C.359 Ligands: S3H.5 No protein-ligand interaction detected (PLIP) H2S.7: 5 residues within 4Å: Chain A: C.163, P.322 Ligands: FAD.1, H2S.4, S3H.5 No protein-ligand interaction detected (PLIP) H2S.8: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) H2S.13: 6 residues within 4Å: Chain B: T.324, V.358, C.359 Ligands: FAD.10, S3H.14, H2S.16 No protein-ligand interaction detected (PLIP) H2S.15: 4 residues within 4Å: Chain B: F.164, G.165, C.359 Ligands: S3H.14 No protein-ligand interaction detected (PLIP) H2S.16: 5 residues within 4Å: Chain B: C.163, P.322 Ligands: FAD.10, H2S.13, S3H.14 No protein-ligand interaction detected (PLIP) H2S.17: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

2 x S3H: TRISULFANE(Non-covalent)

S3H.5: 8 residues within 4Å: Chain A: C.163, P.166, P.322, C.359 Ligands: FAD.1, H2S.4, H2S.6, H2S.7 No protein-ligand interaction detected (PLIP) S3H.14: 8 residues within 4Å: Chain B: C.163, P.166, P.322, C.359 Ligands: FAD.10, H2S.13, H2S.15, H2S.16 No protein-ligand interaction detected (PLIP)

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

SO4.9: 3 residues within 4Å: Chain A: M.1, H.6, H.100 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:M.1, A:M.1 Salt bridges: A:H.6, A:H.100 SO4.18: 3 residues within 4Å: Chain B: M.1, H.6, H.100 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:M.1, B:M.1 Salt bridges: B:H.6, B:H.100

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cherney, M.M. et al., Structure-activity characterization of sulfide:quinone oxidoreductase variants. J.Struct.Biol. (2012)

Release Date

2012-05-16

Peptides

Sulfide-quinone reductase, putative: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Sulfide-quinone reductase, putative