SMTL ID : 6fp4.1

Thioredoxin glutathione reductase from Schistosoma mansoni in complex with 1,8-Naphthyridine-2-carboxylic acid

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

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

FAD.1: 47 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 Ligands: NA.5 30 PLIP interactions: 27 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:T.153, A:F.280, A:V.297 Hydrogen bonds: A:G.115, A:S.117, A:S.117, A:G.118, A:G.119, A:L.136, A:D.137, A:Y.138, 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, A:T.442, B:H.571 Water bridges: A:E.259, A:A.445, B:H.571, B:H.571 pi-Stacking: A:Y.296, A:Y.296 FAD.7: 47 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 Ligands: NA.11 29 PLIP interactions: 26 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:T.153, B:F.280, B:V.297 Hydrogen bonds: B:G.115, B:S.117, B:S.117, B:G.118, B:G.119, B:L.136, 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:D.433, B:T.442, B:T.442, B:T.442, B:T.442, A:H.571 Water bridges: B:E.259, B:A.445, A:H.571, A:H.571 pi-Stacking: B:Y.296, B:Y.296

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

PGE.2: 5 residues within 4Å: Chain A: L.484, D.488, E.491, K.492 Ligands: 250.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.491, A:K.492 PGE.3: 9 residues within 4Å: Chain A: T.7, W.10, I.48, L.53, N.55, I.59, G.459, A.460, T.461 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.55 PGE.8: 5 residues within 4Å: Chain B: L.484, D.488, E.491, K.492 Ligands: 250.12 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.492 PGE.9: 9 residues within 4Å: Chain B: T.7, W.10, I.48, L.53, N.55, I.59, G.459, A.460, T.461 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.55

2 x E1T: 1,8-naphthyridine-2-carboxylic acid(Non-covalent)

E1T.4: 8 residues within 4Å: Chain A: Y.296, F.324, P.439, Q.440, L.441, T.471, V.473 Ligands: 250.6 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.296, A:Y.296, A:L.441 Hydrogen bonds: A:Q.440, A:T.471 E1T.10: 8 residues within 4Å: Chain B: Y.296, F.324, P.439, Q.440, L.441, T.471, V.473 Ligands: 250.12 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:Y.296, B:Y.296, B:L.441 Hydrogen bonds: B:Q.440, B:T.471

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

NA.5: 6 residues within 4Å: Chain A: T.153, G.258, E.259, R.393, D.433 Ligands: FAD.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.153, A:E.259, A:R.393, A:D.433 Water bridges: A:T.153 NA.11: 6 residues within 4Å: Chain B: T.153, G.258, E.259, R.393, D.433 Ligands: FAD.7 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.259, B:E.259, B:R.393 Water bridges: B:T.153

2 x 250: (2R)-2-hydroxy-3-[4-(2-hydroxyethyl)piperazin-1-yl]propane-1-sulfonic acid(Non-covalent)

250.6: 13 residues within 4Å: Chain A: G.323, F.324, D.325, P.439, L.441, Y.466, S.467, N.468, V.469, T.471, L.484 Ligands: PGE.2, E1T.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.466, A:N.468, A:V.469 250.12: 13 residues within 4Å: Chain B: G.323, F.324, D.325, P.439, L.441, Y.466, S.467, N.468, V.469, T.471, L.484 Ligands: PGE.8, E1T.10 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.466, B:N.468, B:V.469

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Silvestri, I. et al., Fragment-Based Discovery of a Regulatory Site in Thioredoxin Glutathione Reductase Acting as "Doorstop" for NADPH Entry. ACS Chem. Biol. (2018)

Release Date

2018-06-06

Peptides

Thioredoxin glutathione reductase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Thioredoxin glutathione reductase

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