SMTL ID : 3t14.1

Crystal structure of sulfide:quinone oxidoreductase Cys128Ala variant from Acidithiobacillus ferrooxidans with bound disulfide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.21 Å

Oligo State

homo-dimer

Ligands

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

FAD.1: 35 residues within 4Å: Chain A: L.10, G.11, A.12, G.13, T.14, G.15, 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.163, P.166, V.270, G.304, I.305, K.323, T.324, G.325, I.328, V.358, C.359, F.360, K.394 Ligands: H2S.4, S2H.5 26 PLIP interactions: 26 interactions with chain A Hydrophobic interactions: A:V.45, A:I.130, A:P.166, A:P.166 Hydrogen bonds: A:A.12, A:A.12, A:T.14, A:T.14, A:G.15, 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:G.16, A:N.39, A:S.80, A:G.109, A:A.306, A:Y.326, A:K.394 FAD.8: 35 residues within 4Å: Chain B: L.10, G.11, A.12, G.13, T.14, G.15, 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.163, P.166, V.270, G.304, I.305, K.323, T.324, G.325, I.328, V.358, C.359, F.360, K.394 Ligands: H2S.11, S2H.12 26 PLIP interactions: 26 interactions with chain B Hydrophobic interactions: B:V.45, B:I.130, B:P.166, B:P.166 Hydrogen bonds: B:A.12, B:A.12, B:T.14, B:T.14, B:G.15, B:S.37, B:A.38, B:N.39, B:A.81, B:A.81, B:I.305, B:G.325, B:F.360, B:K.394 Water bridges: B:G.13, B:G.16, B:N.39, B:S.80, B:G.109, B:A.306, B:Y.326, 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, E.220, C.359, F.360, A.361, M.363, A.368, A.369, F.370, F.384, Y.386 Chain B: G.208, D.209 14 PLIP interactions: 13 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:Y.168, A:I.213, A:L.214, A:L.214, A:A.361, A:F.370, A:F.370, A:F.384, A:Y.386 Hydrogen bonds: A:E.220, A:Y.386 Water bridges: A:G.217, A:Y.386, B:D.209 LMT.9: 17 residues within 4Å: Chain A: G.208, D.209 Chain B: G.165, Y.168, M.172, I.213, L.214, E.220, C.359, F.360, A.361, M.363, A.368, A.369, F.370, F.384, Y.386 16 PLIP interactions: 14 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:Y.168, B:I.213, B:L.214, B:L.214, B:A.361, B:F.370, B:F.370, B:F.384, B:Y.386 Hydrogen bonds: B:E.220, B:Y.386 Water bridges: B:G.217, B:Y.386, B:Y.386, A:D.209, A:D.209

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

SO4.3: 4 residues within 4Å: Chain A: M.1, H.6, H.100, D.102 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:M.1, A:M.1 Water bridges: A:H.100, A:H.100 Salt bridges: A:H.6, A:H.100 SO4.6: 5 residues within 4Å: Chain A: H.337, R.346, K.347, G.348, E.349 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.347, A:E.349, A:Q.350 Salt bridges: A:H.337, A:R.346 SO4.7: 5 residues within 4Å: Chain A: R.66, F.76, I.77, A.78, Q.79 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:A.78, A:Q.79 Water bridges: A:R.66, A:R.66 Salt bridges: A:R.66 SO4.10: 4 residues within 4Å: Chain B: M.1, H.6, H.100, D.102 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:M.1, B:M.1 Water bridges: B:H.100, B:H.100 Salt bridges: B:H.6, B:H.100 SO4.13: 5 residues within 4Å: Chain B: H.337, R.346, K.347, G.348, E.349 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:K.347, B:E.349, B:Q.350 Salt bridges: B:H.337, B:R.346 SO4.14: 5 residues within 4Å: Chain B: R.66, F.76, I.77, A.78, Q.79 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:A.78, B:Q.79 Water bridges: B:R.66, B:R.66 Salt bridges: B:R.66

2 x H2S: HYDROSULFURIC ACID(Non-covalent)

H2S.4: 4 residues within 4Å: Chain A: C.163, P.322 Ligands: FAD.1, S2H.5 No protein-ligand interaction detected (PLIP) H2S.11: 4 residues within 4Å: Chain B: C.163, P.322 Ligands: FAD.8, S2H.12 No protein-ligand interaction detected (PLIP)

2 x S2H: Hydrogen disulfide(Non-covalent)

S2H.5: 5 residues within 4Å: Chain A: G.165, P.166, C.359 Ligands: FAD.1, H2S.4 No protein-ligand interaction detected (PLIP) S2H.12: 5 residues within 4Å: Chain B: G.165, P.166, C.359 Ligands: FAD.8, H2S.11 No protein-ligand interaction detected (PLIP)

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

Related Entries With Identical Sequence