SMTL ID : 8pdd.1

Thioredoxin glutathione reductase of Schistosoma mansoni at 1.25A resolution.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.25 Å

Oligo State

homo-dimer

Ligands

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

FAD.1: 36 residues within 4Å: Chain A: I.114, G.115, G.116, G.117, S.118, G.119, L.137, D.138, Y.139, V.140, G.153, T.154, C.155, V.158, G.159, C.160, K.163, A.227, K.228, G.229, A.257, T.258, G.259, Y.297, V.298, R.394, V.401, G.433, D.434, Q.441, L.442, T.443, P.444, F.475 Chain B: H.572, P.573 36 PLIP interactions: 34 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:T.154, A:V.298 Hydrogen bonds: A:G.116, A:S.118, A:S.118, A:G.119, A:D.138, A:Y.139, A:G.153, A:T.154, A:T.154, A:C.155, A:K.163, A:G.229, A:G.229, A:D.434, A:Q.441, A:T.443, A:T.443, A:T.443, B:H.572 Water bridges: A:G.117, A:G.120, A:D.138, A:D.138, A:E.141, A:G.259, A:E.260, A:E.260, A:R.261, A:D.434, A:I.435, A:A.446, B:H.572 pi-Stacking: A:Y.297, A:Y.297 FAD.13: 36 residues within 4Å: Chain A: H.572, P.573 Chain B: I.114, G.115, G.116, G.117, S.118, G.119, L.137, D.138, Y.139, V.140, G.153, T.154, C.155, V.158, G.159, C.160, K.163, A.227, K.228, G.229, A.257, T.258, G.259, Y.297, V.298, R.394, V.401, G.433, D.434, Q.441, L.442, T.443, P.444, F.475 33 PLIP interactions: 31 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:V.298 Hydrogen bonds: B:G.116, B:S.118, B:S.118, B:G.119, B:Y.139, B:T.154, B:T.154, B:T.154, B:C.155, B:K.163, B:G.229, B:G.229, B:D.434, B:Q.441, B:T.443, B:T.443, B:T.443, A:H.572 Water bridges: B:G.117, B:G.120, B:D.138, B:E.141, B:G.153, B:G.259, B:E.260, B:E.260, B:R.261, B:I.435, B:A.446, A:H.572 pi-Stacking: B:Y.297, B:Y.297

3 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 1 residues within 4Å: Chain A: H.515 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:H.515, H2O.7, H2O.11, H2O.22, H2O.22, H2O.29 MG.3: 3 residues within 4Å: Chain A: L.485, S.486, D.489 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.489, H2O.13, H2O.20 MG.14: 1 residues within 4Å: Chain B: H.515 6 PLIP interactions: 1 interactions with chain B, 5 Ligand-Water interactions Metal complexes: B:H.515, H2O.26, H2O.31, H2O.38, H2O.47, H2O.48

15 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 6 residues within 4Å: Chain A: Y.297, P.440, Q.441, L.442, T.472 Ligands: GOL.10 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.441 Water bridges: A:Y.297 GOL.5: 4 residues within 4Å: Chain A: S.468, N.469, G.484, L.485 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.469, A:G.484 Water bridges: A:N.469, A:V.470 GOL.6: 7 residues within 4Å: Chain A: K.14, S.18, D.421, Y.430, L.453, R.456, L.457 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.18, A:S.18, A:D.421, A:Y.430, A:Y.430, A:R.456, A:R.456 GOL.7: 6 residues within 4Å: Chain A: E.141, P.142, T.143, P.144, R.261, Q.397 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.141, A:Q.397 Water bridges: A:E.141, A:P.262, A:E.395 GOL.8: 6 residues within 4Å: Chain A: Q.448, Y.452, R.455 Chain B: D.566, T.580, T.581 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Q.448, A:R.455, A:R.455, B:D.566 Water bridges: A:R.451, A:Y.452 GOL.9: 4 residues within 4Å: Chain A: S.68, K.69, I.70, F.82 No protein-ligand interaction detected (PLIP) GOL.10: 5 residues within 4Å: Chain A: S.296, Y.297, G.393, R.394 Ligands: GOL.4 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.296, A:S.296, A:R.394 Water bridges: A:E.260, A:G.393 GOL.11: 5 residues within 4Å: Chain A: I.320, L.321, Q.327, A.330, E.331 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.319, A:L.321, A:Q.327 GOL.12: 8 residues within 4Å: Chain A: V.21, K.43, I.44, K.45, R.79, V.102, N.103, G.131 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:K.45, A:K.45, A:R.79, A:R.79, A:N.103 Water bridges: A:K.45, A:K.45, A:K.45 GOL.15: 6 residues within 4Å: Chain B: Y.297, P.440, Q.441, L.442, T.472 Ligands: GOL.16 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.441 Water bridges: B:Y.297 GOL.16: 5 residues within 4Å: Chain B: S.296, Y.297, G.393, R.394 Ligands: GOL.15 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.296, B:R.394 Water bridges: B:G.393 GOL.17: 6 residues within 4Å: Chain B: E.141, P.142, T.143, P.144, R.261, Q.397 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.397 Water bridges: B:P.262, B:E.395 GOL.18: 6 residues within 4Å: Chain B: S.18, D.421, Y.430, L.453, R.456, L.457 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.18, B:D.421, B:R.456, B:R.456 GOL.19: 5 residues within 4Å: Chain B: Y.139, K.228, T.240, D.241, Q.244 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.228, B:T.240, B:D.241, B:Q.244 GOL.20: 4 residues within 4Å: Chain B: S.468, N.469, G.484, L.485 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.469, B:G.484 Water bridges: B:V.470, B:V.470, B:G.484

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

de Souza Neto, L.R. et al., Fragment library screening by X-ray crystallography and binding site analysis on thioredoxin glutathione reductase of Schistosoma mansoni. Sci Rep (2024)

Release Date

2024-01-31

Peptides

Thioredoxin glutathione reductase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Thioredoxin glutathione reductase

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