SMTL ID : 7b02.1

Thioredoxin glutathione reductase from Schistosoma mansoni in complex with 4-Hydroxy-7-methyl-1,8-naphthyridine-3-carboxylic acid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

homo-dimer

Ligands

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

FAD.1: 35 residues within 4Å: Chain A: I.113, G.114, G.115, G.116, S.117, G.118, L.136, D.137, Y.138, V.139, 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, Y.296, V.297, R.393, V.400, G.432, D.433, Q.440, L.441, T.442, P.443 Chain B: H.571, P.572 39 PLIP interactions: 36 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: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:Y.296, 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:W.148, A:G.152, A:G.258, A:E.259, A:E.259, A:R.260, A:R.260, A:D.433, A:I.434, A:A.445, B:H.571, B:H.571 pi-Stacking: A:Y.296, A:Y.296 FAD.11: 35 residues within 4Å: Chain A: H.571, P.572 Chain B: I.113, G.114, G.115, G.116, S.117, G.118, L.136, D.137, Y.138, V.139, 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, Y.296, V.297, R.393, V.400, G.432, D.433, Q.440, L.441, T.442, P.443 37 PLIP interactions: 34 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:Y.138, 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, B:T.442, A:H.571 Water bridges: B:G.115, B:G.116, B:G.119, B:E.140, B:W.148, B:G.152, B:T.153, B:G.258, B:E.259, B:E.259, B:R.260, B:R.260, B:I.434, B:A.445, A:H.571, A:H.571 pi-Stacking: B:Y.296, B:Y.296

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

PEG.2: 4 residues within 4Å: Chain A: Y.223, L.224, N.225, D.240 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.225 Water bridges: A:Y.223, A:D.240 PEG.3: 6 residues within 4Å: Chain A: Y.138, N.225, T.239, D.240, K.241, Q.243 No protein-ligand interaction detected (PLIP) PEG.8: 3 residues within 4Å: Chain A: R.317, S.318, R.322 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.322 Water bridges: A:R.317, A:I.319 PEG.10: 6 residues within 4Å: Chain A: L.320, G.333, D.334, E.337, F.343, K.345 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.334, A:E.337, A:K.345 Water bridges: A:V.316, A:S.318 PEG.12: 4 residues within 4Å: Chain B: Y.223, L.224, N.225, D.240 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.225 Water bridges: B:Y.223, B:D.240, B:D.240 PEG.13: 6 residues within 4Å: Chain B: Y.138, N.225, T.239, D.240, K.241, Q.243 No protein-ligand interaction detected (PLIP) PEG.18: 3 residues within 4Å: Chain B: R.317, S.318, R.322 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.322 Water bridges: B:R.317, B:I.319 PEG.20: 6 residues within 4Å: Chain B: L.320, G.333, D.334, E.337, F.343, K.345 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:E.337, B:E.337, B:K.345 Water bridges: B:V.316, B:S.318

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

DMS.4: 4 residues within 4Å: Chain A: E.140, P.141, R.260, K.399 2 PLIP interactions: 2 interactions with chain A Water bridges: A:K.399 Salt bridges: A:E.140 DMS.14: 4 residues within 4Å: Chain B: E.140, P.141, R.260, K.399 2 PLIP interactions: 2 interactions with chain B Water bridges: B:K.399 Salt bridges: B:E.140

2 x SJN: 4-Hydroxy-7-methyl-1,8-naphthyridine-3-carboxylic acid(Non-covalent)

SJN.5: 5 residues within 4Å: Chain A: K.353, L.355, L.369, E.381, E.383 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.369, A:L.369, A:E.381 Hydrogen bonds: A:E.383, A:E.383 Water bridges: A:K.371 Salt bridges: A:K.353 SJN.15: 5 residues within 4Å: Chain B: K.353, L.355, L.369, E.381, E.383 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:L.369, B:L.369, B:E.381 Hydrogen bonds: B:E.383 Water bridges: B:K.371 Salt bridges: B:K.353

2 x K: POTASSIUM ION(Non-covalent)

K.6: 4 residues within 4Å: Chain A: D.565, T.567, T.579 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.14 K.16: 4 residues within 4Å: Chain A: Q.447 Chain B: D.565, T.567, T.579 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.565, B:T.567, B:T.579, H2O.40

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

CL.7: 4 residues within 4Å: Chain A: G.149, L.150, N.209, K.213 Ligand excluded by PLIP CL.17: 4 residues within 4Å: Chain B: G.149, L.150, N.209, K.213 Ligand excluded by PLIP

2 x NA: SODIUM ION(Non-functional Binders)

NA.9: 4 residues within 4Å: Chain A: Y.451, E.462 Chain B: D.565, R.566 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Water bridges: A:E.462 Hydrogen bonds: B:D.565 NA.19: 4 residues within 4Å: Chain A: D.565, R.566 Chain B: Y.451, E.462 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.451, B:E.462

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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