SMTL ID : 6zp3.1

Thioredoxin glutathione reductase from Schistosoma mansoni in complex with 2-Methylindole-3-acetic acid

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

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

FAD.1: 43 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, G.432, D.433, Q.440, L.441, T.442, P.443, A.445, F.474 Chain B: H.571, P.572 34 PLIP interactions: 31 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:T.153, A:V.297 Hydrogen bonds: A:G.115, 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:D.433, A:T.442, A:T.442, A:T.442, B:H.571 Water bridges: A:G.115, A:G.116, A:E.140, A:G.152, A:G.258, A:G.258, A:E.259, A:R.260, A:A.445, B:H.571, B:H.571 pi-Stacking: A:Y.296 FAD.10: 43 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, G.432, D.433, Q.440, L.441, T.442, P.443, A.445, F.474 33 PLIP interactions: 30 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:T.153, B:V.297 Hydrogen bonds: B:G.115, 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:D.433, B:T.442, B:T.442, B:T.442, A:H.571 Water bridges: B:G.115, B:G.116, B:E.140, B:G.152, B:G.258, B:G.258, B:E.259, B:R.260, B:A.445, A:H.571, A:H.571 pi-Stacking: B:Y.296

2 x K: POTASSIUM ION(Non-covalent)

K.2: 4 residues within 4Å: Chain A: G.293, R.317, V.391 Ligands: QN5.5 No protein-ligand interaction detected (PLIP) K.11: 4 residues within 4Å: Chain B: G.293, R.317, V.391 Ligands: QN5.14 No protein-ligand interaction detected (PLIP)

2 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.3: 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 PG4.12: 4 residues within 4Å: Chain B: L.484, D.488, E.491, K.492 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.488, B:K.492

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

DMS.4: 10 residues within 4Å: Chain A: K.561, D.565, T.579, T.580, L.581, H.582 Chain B: Q.447, Y.451, R.454 Ligands: CA.6 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.454, B:R.454 Salt bridges: A:D.565 DMS.13: 10 residues within 4Å: Chain A: Q.447, Y.451, R.454 Chain B: K.561, D.565, T.579, T.580, L.581, H.582 Ligands: CA.15 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.454, A:R.454 Salt bridges: B:D.565

2 x QN5: 2-(2-methyl-1~{H}-indol-3-yl)ethanoic acid(Non-covalent)

QN5.5: 6 residues within 4Å: Chain A: R.317, S.318, I.319, R.322, V.391 Ligands: K.2 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.318, A:S.318 Water bridges: A:R.317, A:I.319 Salt bridges: A:R.317, A:R.322 QN5.14: 6 residues within 4Å: Chain B: R.317, S.318, I.319, R.322, V.391 Ligands: K.11 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:S.318, B:S.318 Water bridges: B:R.317, B:I.319 Salt bridges: B:R.317, B:R.322

2 x CA: CALCIUM ION(Non-covalent)

CA.6: 7 residues within 4Å: Chain A: D.565, T.567, I.568, T.579, T.580 Chain B: Q.447 Ligands: DMS.4 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 CA.15: 7 residues within 4Å: Chain A: Q.447 Chain B: D.565, T.567, I.568, T.579, T.580 Ligands: DMS.13 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.565, B:T.567, B:T.579, H2O.21

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.7: 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 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.330 Water bridges: A:L.320 PEG.16: 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 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.330 Water bridges: B:L.320

2 x DTT: 2,3-DIHYDROXY-1,4-DITHIOBUTANE(Non-covalent)

DTT.8: 10 residues within 4Å: Chain A: G.228, R.229, L.230, L.255, Q.396, L.397, S.398, L.401, C.402, V.407 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.230 Water bridges: A:G.228 DTT.17: 10 residues within 4Å: Chain B: G.228, R.229, L.230, L.255, Q.396, L.397, S.398, L.401, C.402, V.407 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:L.230 Water bridges: B:G.228

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

PGE.9: 9 residues within 4Å: Chain A: Q.327, K.331, H.502, N.504, N.518, Y.521, K.585, P.591, I.592 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Q.327, A:K.331, A:H.502, A:N.504, A:K.585 Water bridges: A:N.518 PGE.18: 9 residues within 4Å: Chain B: Q.327, K.331, H.502, N.504, N.518, Y.521, K.585, P.591, I.592 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Q.327, B:K.331, B:H.502, B:N.504, B:K.585 Water bridges: B:N.518

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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