SMTL ID : 6rtm.1

Thioredoxin glutathione reductase from Schistosoma mansoni in complex with 1-[(dimethylamino)methyl]-2-naphthol at 2 hour of soaking

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

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

FAD.1: 46 residues within 4Å: Chain A: I.113, G.114, G.115, G.116, S.117, G.118, G.119, L.136, D.137, Y.138, V.139, E.140, W.148, G.152, T.153, C.154, V.157, G.158, C.159, K.162, A.226, K.227, G.228, A.256, T.257, G.258, E.259, R.260, S.276, F.280, Y.296, V.297, E.300, R.393, K.399, V.400, G.432, D.433, Q.440, L.441, T.442, P.443, A.445, F.474 Chain B: H.571, P.572 37 PLIP interactions: 34 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:T.153, A:V.297, A:V.297 Hydrogen bonds: A:G.114, A:G.115, A:S.117, A:S.117, A:G.118, A:D.137, A:D.137, A:Y.138, A:T.153, A:T.153, A:T.153, A:C.154, A:K.162, A:G.228, A:G.228, A:D.433, A:Q.440, A:T.442, A:T.442, B:H.571 Water bridges: A:G.115, A:G.116, A:G.119, A:E.140, A:G.152, A:T.257, A:G.258, A:E.259, A:E.259, A:D.433, A:I.434, A:L.441, B:H.571, B:H.571 FAD.6: 46 residues within 4Å: Chain A: H.571, P.572 Chain B: I.113, G.114, G.115, G.116, S.117, G.118, G.119, L.136, D.137, Y.138, V.139, E.140, W.148, G.152, T.153, C.154, V.157, G.158, C.159, K.162, A.226, K.227, G.228, A.256, T.257, G.258, E.259, R.260, S.276, F.280, Y.296, V.297, E.300, R.393, K.399, V.400, G.432, D.433, Q.440, L.441, T.442, P.443, A.445, F.474 36 PLIP interactions: 33 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:T.153, B:V.297, B:V.297 Hydrogen bonds: B:G.114, B:G.115, B:S.117, B:S.117, B:G.118, B:D.137, B:Y.138, B:T.153, B:T.153, B:T.153, B:C.154, B:K.162, B:G.228, B:G.228, B:D.433, B:Q.440, B:T.442, B:T.442, A:H.571 Water bridges: B:G.115, B:G.116, B:G.119, B:E.140, B:G.152, B:T.257, B:G.258, B:E.259, B:E.259, B:E.259, B:D.433, B:I.434, A:H.571, A:H.571

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

PGE.2: 4 residues within 4Å: Chain A: L.484, D.488, E.491, K.492 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.492 PGE.3: 8 residues within 4Å: Chain A: Y.138, N.225, A.226, K.227, T.239, D.240, K.241, Q.243 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.225 PGE.7: 4 residues within 4Å: Chain B: L.484, D.488, E.491, K.492 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.492 PGE.8: 8 residues within 4Å: Chain B: Y.138, N.225, A.226, K.227, T.239, D.240, K.241, Q.243 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.225

2 x K: POTASSIUM ION(Non-covalent)

K.4: 6 residues within 4Å: Chain A: D.565, T.567, I.568, T.579, T.580 Chain B: Q.447 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.565, A:T.567, A:T.579, H2O.8 K.9: 6 residues within 4Å: Chain A: Q.447 Chain B: D.565, T.567, I.568, T.579, T.580 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.565, B:T.567, B:T.579, H2O.20

2 x KJH: 1-methylidenenaphthalen-2-one(Non-covalent)

KJH.5: 10 residues within 4Å: Chain A: V.316, S.318, I.319, L.320, E.330, G.333, D.334, E.337, F.343, K.345 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:V.316, A:V.316, A:L.320, A:L.320, A:L.320, A:E.330, A:F.343, A:K.345 Hydrogen bonds: A:E.330 pi-Stacking: A:F.343 KJH.10: 10 residues within 4Å: Chain B: V.316, S.318, I.319, L.320, E.330, G.333, D.334, E.337, F.343, K.345 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:V.316, B:V.316, B:L.320, B:L.320, B:L.320, B:E.330, B:F.343, B:K.345 pi-Stacking: B:F.343

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Silvestri, I. et al., Ectopic suicide inhibition of thioredoxin glutathione reductase. Free Radic Biol Med (2020)

Release Date

2020-01-08

Peptides

Thioredoxin glutathione reductase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Thioredoxin glutathione reductase

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