SMTL ID : 4v2k.1

Crystal structure of the thiosulfate dehydrogenase TsdA in complex with thiosulfate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.29 Å

Oligo State

homo-dimer

Ligands

4 x HEC: HEME C(Covalent)

HEC.1: 19 residues within 4Å: Chain A: L.47, H.51, C.52, P.54, R.159, C.160, C.163, H.164, L.179, F.180, P.181, P.182, L.183, F.189, F.204, I.205, M.209, P.210, L.211 9 PLIP interactions: 9 interactions with chain A, Hydrophobic interactions: A:F.180, A:P.181, A:L.183, A:L.183, A:F.204, A:I.205, A:M.209, A:L.211 Metal complexes: A:H.164 HEC.2: 22 residues within 4Å: Chain A: L.32, A.48, C.49, C.52, H.53, A.67, F.69, V.72, F.76, L.89, R.92, C.96, F.97, S.100, L.101, M.120, G.137, I.138, F.189, M.195, T.200 Ligands: THJ.3 19 PLIP interactions: 19 interactions with chain A, Hydrophobic interactions: A:L.32, A:A.67, A:F.69, A:V.72, A:L.89, A:F.97, A:L.101, A:L.101, A:I.138, A:F.189, A:M.195, A:T.200 Hydrogen bonds: A:I.138 Water bridges: A:P.68, A:P.68, A:Q.78, A:Q.78 pi-Stacking: A:H.53 Metal complexes: A:H.53 HEC.4: 19 residues within 4Å: Chain B: L.47, H.51, C.52, P.54, R.159, C.160, C.163, H.164, L.179, F.180, P.181, P.182, L.183, F.189, F.204, I.205, M.209, P.210, L.211 9 PLIP interactions: 9 interactions with chain B, Hydrophobic interactions: B:F.180, B:P.181, B:L.183, B:L.183, B:F.204, B:I.205, B:M.209, B:L.211 Metal complexes: B:H.164 HEC.5: 22 residues within 4Å: Chain B: L.32, A.48, C.49, C.52, H.53, A.67, F.69, V.72, F.76, L.89, R.92, C.96, F.97, S.100, L.101, M.120, G.137, I.138, F.189, M.195, T.200 Ligands: THJ.6 19 PLIP interactions: 19 interactions with chain B, Hydrophobic interactions: B:L.32, B:A.67, B:F.69, B:V.72, B:L.89, B:F.97, B:L.101, B:L.101, B:I.138, B:F.189, B:M.195, B:T.200 Hydrogen bonds: B:I.138 Water bridges: B:P.68, B:P.68, B:Q.78, B:Q.78 pi-Stacking: B:H.53 Metal complexes: B:H.53

2 x THJ: THIOSULFATE(Non-covalent)

THJ.3: 10 residues within 4Å: Chain A: R.82, R.92, D.95, C.96, R.99, S.100, G.192, A.193, G.194 Ligands: HEC.2 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.100, A:G.192, A:G.194 Water bridges: A:R.92, A:R.92 Salt bridges: A:R.82, A:R.92 THJ.6: 10 residues within 4Å: Chain B: R.82, R.92, D.95, C.96, R.99, S.100, G.192, A.193, G.194 Ligands: HEC.5 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:S.100, B:G.192, B:G.194 Water bridges: B:R.92, B:R.92 Salt bridges: B:R.82, B:R.92

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Grabarczyk, D.B. et al., Mechanism of Thiosulfate Oxidation in the Soxa Family of Cysteine-Ligated Cytochromes. J.Biol.Chem. (2015)

Release Date

2015-02-18

Peptides

THIOSULFATE DEHYDROGENASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

THIOSULFATE DEHYDROGENASE