SMTL ID : 5lo9.1

Thiosulfate dehydrogenase (TsdBA) from Marichromatium purpuratum - "as isolated" form

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.75 Å

Oligo State

homo-dimer

Ligands

8 x HEC: HEME C(Covalent)

HEC.1: 27 residues within 4Å: Chain A: V.19, A.20, C.21, C.24, H.25, L.35, G.36, A.37, A.38, L.40, L.43, Y.47, L.48, Q.51, I.52, F.55, R.60, H.62, V.64, M.65, W.68, L.72, V.80, Q.142, Y.146, Q.150 Ligands: HEC.2 20 PLIP interactions: 20 interactions with chain A, Hydrophobic interactions: A:V.19, A:A.38, A:L.40, A:L.40, A:L.48, A:I.52, A:H.62, A:V.64, A:L.72, A:V.80, A:Y.146 Hydrogen bonds: A:Q.142, A:Y.146, A:Q.150 Water bridges: A:G.36, A:H.62 Salt bridges: A:R.60, A:R.60, A:H.62 Metal complexes: A:H.25 HEC.2: 26 residues within 4Å: Chain A: Y.47, Q.51, R.54, A.120, C.121, C.124, H.125, V.135, F.136, P.137, L.139, Q.142, Y.146, L.147, Q.150, L.151, W.154, R.159, E.162, L.166, M.167, V.170, L.182, L.453 Ligands: HEC.1, HEC.4 18 PLIP interactions: 18 interactions with chain A, Hydrophobic interactions: A:F.136, A:L.139, A:L.147, A:Q.150, A:L.151, A:W.154, A:E.162, A:L.166, A:L.182, A:L.453 Hydrogen bonds: A:Q.51, A:Q.142, A:Y.146 Salt bridges: A:R.54, A:R.60, A:R.159, A:R.159 Metal complexes: A:H.125 HEC.3: 21 residues within 4Å: Chain A: F.268, T.286, C.287, C.290, H.291, M.303, A.306, Y.310, M.323, R.326, C.330, F.331, S.334, M.335, R.377, Y.379, Y.430, M.436, T.441 Ligands: HEC.4, THJ.8 13 PLIP interactions: 13 interactions with chain A, Hydrophobic interactions: A:F.268, A:A.306, A:F.331, A:Y.379, A:Y.430, A:M.436, A:T.441 Hydrogen bonds: A:Y.310 Water bridges: A:G.378 Salt bridges: A:K.316, A:R.326, A:R.377 Metal complexes: A:H.291 HEC.4: 29 residues within 4Å: Chain A: R.123, C.124, M.164, R.269, Q.285, A.288, G.289, C.290, L.292, H.401, C.402, C.405, H.406, V.420, F.421, P.422, P.423, L.424, Y.430, F.445, I.446, M.450, P.451, L.452, L.458, V.466, I.470 Ligands: HEC.2, HEC.3 17 PLIP interactions: 17 interactions with chain A, Hydrophobic interactions: A:R.123, A:L.292, A:F.421, A:P.422, A:L.424, A:F.445, A:F.445, A:I.446, A:M.450, A:L.452, A:L.458, A:V.466, A:I.470 Hydrogen bonds: A:Q.285 Salt bridges: A:R.123, A:R.269 Metal complexes: A:H.406 HEC.27: 26 residues within 4Å: Chain B: V.19, A.20, C.21, C.24, H.25, L.35, G.36, A.37, A.38, L.40, L.43, Y.47, L.48, Q.51, F.55, R.60, H.62, V.64, M.65, W.68, L.72, V.80, Q.142, Y.146, Q.150 Ligands: HEC.28 19 PLIP interactions: 19 interactions with chain B, Hydrophobic interactions: B:V.19, B:A.38, B:L.40, B:L.40, B:L.48, B:F.55, B:H.62, B:V.64, B:M.65, B:L.72, B:V.80, B:Y.146 Hydrogen bonds: B:Y.47, B:Q.142, B:Q.150 Salt bridges: B:R.60, B:R.60, B:H.62 Metal complexes: B:H.25 HEC.28: 25 residues within 4Å: Chain B: Y.47, Q.51, R.54, A.120, C.121, C.124, H.125, V.135, F.136, P.137, L.139, Q.142, Y.146, L.147, Q.150, L.151, W.154, R.159, E.162, L.166, M.167, V.170, L.182 Ligands: HEC.27, HEC.30 19 PLIP interactions: 19 interactions with chain B, Hydrophobic interactions: B:F.136, B:L.139, B:L.147, B:L.151, B:W.154, B:W.154, B:E.162, B:L.166, B:V.170 Hydrogen bonds: B:Y.47, B:Q.51, B:Q.142 Salt bridges: B:R.54, B:R.60, B:R.159, B:R.159 pi-Stacking: B:H.125, B:H.125 Metal complexes: B:H.125 HEC.29: 23 residues within 4Å: Chain B: F.268, T.286, C.287, C.290, H.291, S.301, M.303, A.306, Y.310, M.323, R.326, C.330, F.331, S.334, M.335, R.377, G.378, Y.379, Y.430, M.436, T.441 Ligands: HEC.30, THJ.32 14 PLIP interactions: 14 interactions with chain B, Hydrophobic interactions: B:F.268, B:A.306, B:Y.310, B:F.331, B:Y.379, B:Y.430, B:M.436, B:T.441 Hydrogen bonds: B:Y.310, B:Y.379 Water bridges: B:S.301, B:G.378 Salt bridges: B:R.377 Metal complexes: B:H.291 HEC.30: 29 residues within 4Å: Chain B: R.123, M.164, L.166, R.269, Q.285, A.288, G.289, C.290, L.292, H.401, C.402, C.405, H.406, V.420, F.421, P.422, P.423, L.424, Y.430, F.445, I.446, M.450, P.451, L.452, L.458, V.466, I.470 Ligands: HEC.28, HEC.29 21 PLIP interactions: 21 interactions with chain B, Hydrophobic interactions: B:R.123, B:L.166, B:L.292, B:H.401, B:F.421, B:P.422, B:L.424, B:F.445, B:F.445, B:I.446, B:M.450, B:P.451, B:L.452, B:L.458, B:V.466, B:I.470 Hydrogen bonds: B:Q.285 Water bridges: B:G.289 Salt bridges: B:R.123, B:R.269 Metal complexes: B:H.406

11 x CL: CHLORIDE ION(Non-functional Binders)

CL.5: 3 residues within 4Å: Chain A: W.113, A.120, R.123 Ligand excluded by PLIP CL.6: 2 residues within 4Å: Chain A: W.154, G.168 Ligand excluded by PLIP CL.9: 1 residues within 4Å: Chain A: R.158 Ligand excluded by PLIP CL.10: 1 residues within 4Å: Ligands: EDO.21 Ligand excluded by PLIP CL.11: 2 residues within 4Å: Chain A: P.427, R.428 Ligand excluded by PLIP CL.12: 2 residues within 4Å: Chain A: G.131, G.133 Ligand excluded by PLIP CL.13: 1 residues within 4Å: Chain A: D.339 Ligand excluded by PLIP CL.31: 3 residues within 4Å: Chain B: W.113, A.120, R.123 Ligand excluded by PLIP CL.33: 2 residues within 4Å: Chain B: L.35, H.62 Ligand excluded by PLIP CL.34: 2 residues within 4Å: Chain B: R.249 Ligands: CL.35 Ligand excluded by PLIP CL.35: 3 residues within 4Å: Chain B: R.249, N.294 Ligands: CL.34 Ligand excluded by PLIP

4 x PGO: S-1,2-PROPANEDIOL(Non-covalent)

PGO.7: 4 residues within 4Å: Chain A: T.50, R.54, G.161, P.163 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:P.163 Hydrogen bonds: A:R.54, A:R.54 PGO.14: 4 residues within 4Å: Chain A: G.155, A.171, G.172, L.174 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.155, A:L.174 PGO.36: 4 residues within 4Å: Chain B: D.339, P.427, R.428, V.515 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:P.427, B:R.428 PGO.37: 4 residues within 4Å: Chain B: F.244, P.246, R.296, A.298 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:A.298 Hydrogen bonds: B:F.244

2 x THJ: THIOSULFATE(Non-covalent)

THJ.8: 9 residues within 4Å: Chain A: K.316, R.326, G.329, C.330, Y.333, S.334, A.434, G.435 Ligands: HEC.3 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.334, A:G.435 Water bridges: A:M.436 Salt bridges: A:K.316, A:R.326 THJ.32: 9 residues within 4Å: Chain B: K.316, R.326, G.329, C.330, Y.333, S.334, A.434, G.435 Ligands: HEC.29 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.334, B:G.435 Salt bridges: B:K.316, B:R.326

12 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.15: 5 residues within 4Å: Chain A: A.132, V.135, L.404, C.405, G.407 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.404, A:G.412 EDO.16: 5 residues within 4Å: Chain A: A.373, M.374, S.375, G.376, R.377 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.243, A:A.373, A:G.376 EDO.17: 8 residues within 4Å: Chain A: Y.310, P.311, T.322, M.323, A.324, Q.357 Chain B: W.307, Q.357 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.310, A:M.323, A:A.324 EDO.18: 4 residues within 4Å: Chain A: P.114, F.244, P.246, R.296 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:F.244 Water bridges: A:D.293, A:R.296 EDO.19: 4 residues within 4Å: Chain A: R.26, D.32, E.33, N.92 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.26, A:E.33, A:N.92 EDO.20: 3 residues within 4Å: Chain A: Q.338, S.340, V.341 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.340 EDO.21: 6 residues within 4Å: Chain A: R.249, A.265, N.294, R.296, Y.359 Ligands: CL.10 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.249, A:N.294, A:R.296, A:R.296 EDO.22: 3 residues within 4Å: Chain A: W.362, T.365 Chain B: G.370 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.365 EDO.23: 1 residues within 4Å: Chain A: Q.513 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.513 EDO.24: 1 residues within 4Å: Chain A: R.393 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.393 EDO.25: 4 residues within 4Å: Chain A: E.325, Q.328, G.329, R.332 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.328 EDO.38: 5 residues within 4Å: Chain B: R.381, L.382, D.440, W.464, F.497 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:L.382, B:D.440

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.26: 1 residues within 4Å: Chain A: H.160 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.160

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kurth, J.M. et al., Electron Accepting Units of the Diheme Cytochrome c TsdA, a Bifunctional Thiosulfate Dehydrogenase/Tetrathionate Reductase. J.Biol.Chem. (2016)

Release Date

2016-10-12

Peptides

Cytochrome C: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Cytochrome C