SMTL ID : 6zlb.1

Thioredoxin glutathione reductase from Schistosoma mansoni in complex with Indole-3-carbinol

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

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

FAD.1: 44 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, R.393, V.400, G.432, D.433, Q.440, L.441, T.442, P.443, A.445, F.474 Chain B: H.571, P.572 35 PLIP interactions: 33 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:T.153, A:K.162, A:V.297, A:V.297 Hydrogen bonds: A:G.115, A:S.117, A:S.117, A:S.117, A:G.118, A:G.119, 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:L.441, A:T.442, A:T.442, B:H.571 Water bridges: A:G.116, A:D.137, A:E.140, A:G.152, A:K.227, A:G.258, A:G.258, A:E.259, A:A.445, B:H.571 pi-Stacking: A:Y.296 FAD.7: 44 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, R.393, V.400, G.432, D.433, Q.440, L.441, T.442, P.443, A.445, F.474 34 PLIP interactions: 2 interactions with chain A, 32 interactions with chain B Hydrogen bonds: A:H.571, B:G.115, B:S.117, B:S.117, B:S.117, B:G.118, B:G.119, 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:L.441, B:T.442, B:T.442 Water bridges: A:H.571, B:G.116, B:D.137, B:E.140, B:G.152, B:K.227, B:G.258, B:G.258, B:E.259, B:A.445 Hydrophobic interactions: B:T.153, B:K.162, B:V.297, B:V.297 pi-Stacking: B:Y.296

2 x FXK: 1~{H}-indol-3-ylmethanol(Non-covalent)

FXK.2: 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 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:V.316, A:L.320, A:L.320, A:F.343, A:K.345 Hydrogen bonds: A:E.337, A:K.345 Water bridges: A:E.330 FXK.8: 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 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:V.316, B:L.320, B:L.320, B:F.343, B:K.345 Hydrogen bonds: B:E.337, B:K.345

2 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.3: 4 residues within 4Å: Chain A: P.143, I.144, V.270, E.271 No protein-ligand interaction detected (PLIP) DMS.9: 4 residues within 4Å: Chain B: P.143, I.144, V.270, E.271 No protein-ligand interaction detected (PLIP)

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

PGE.4: 10 residues within 4Å: Chain A: Q.327, K.331, H.502, N.504, Y.521, T.584, K.585, G.588, V.589, P.591 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Q.327, A:K.331 Water bridges: A:N.504, A:N.504, A:K.585, A:V.589 PGE.10: 10 residues within 4Å: Chain B: Q.327, K.331, H.502, N.504, Y.521, T.584, K.585, G.588, V.589, P.591 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Q.327, B:K.331 Water bridges: B:N.504, B:N.504, B:K.585, B:V.589

4 x K: POTASSIUM ION(Non-covalent)

K.5: 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.34 K.6: 4 residues within 4Å: Chain A: P.443, I.446, Q.447 Chain B: T.580 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:P.443, H2O.3, H2O.34, H2O.42 K.11: 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.13 K.12: 4 residues within 4Å: Chain A: T.580 Chain B: P.443, I.446, Q.447 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:P.443, H2O.13, H2O.20, H2O.25

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fata, F. et al., Probing the Surface of a Parasite Drug Target Thioredoxin Glutathione Reductase Using Small Molecule Fragments. Acs Infect Dis. (2021)

Release Date

2021-05-19

Peptides

Thioredoxin glutathione reductase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Thioredoxin glutathione reductase

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