SMTL ID : 5s9v.1

PanDDA analysis group deposition -- Crystal Structure of Trypanosoma brucei Trypanothione reductase in complex with Z2856434826

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: 37 residues within 4Å: Chain A: I.13, G.14, G.16, S.17, G.18, V.37, D.38, V.39, A.49, A.50, G.53, T.54, C.55, V.58, G.59, C.60, K.63, G.128, W.129, G.130, A.162, T.163, G.164, S.181, F.201, I.202, R.290, R.293, G.329, D.330, M.336, L.337, T.338, P.339, A.341 Chain B: H.464, P.465 31 PLIP interactions: 29 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:T.54, A:I.202 Hydrogen bonds: A:S.17, A:S.17, A:G.18, A:G.19, A:V.39, A:A.49, A:T.54, A:T.54, A:C.55, A:K.63, A:G.130, A:G.130, A:G.164, A:R.293, A:D.330, A:M.336, A:T.338, A:T.338, B:H.464 Water bridges: A:G.16, A:T.54, A:S.165, A:R.293, A:I.331, A:A.341, A:A.368, B:H.464 pi-Stacking: A:F.201, A:F.201 FAD.11: 37 residues within 4Å: Chain A: H.464, P.465 Chain B: I.13, G.14, G.16, S.17, G.18, G.19, V.37, D.38, V.39, A.49, A.50, G.53, T.54, C.55, V.58, G.59, C.60, K.63, G.128, W.129, G.130, A.162, T.163, G.164, F.201, I.202, R.290, R.293, G.329, D.330, M.336, L.337, T.338, P.339, A.341 33 PLIP interactions: 31 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:T.54, B:I.202 Hydrogen bonds: B:S.17, B:S.17, B:G.18, B:G.19, B:A.49, B:A.50, B:G.53, B:T.54, B:T.54, B:C.55, B:K.63, B:G.130, B:G.130, B:R.293, B:D.330, B:M.336, B:T.338, B:T.338, B:T.338, A:H.464 Water bridges: B:G.16, B:S.17, B:A.49, B:G.52, B:G.164, B:S.165, B:S.165, B:I.331, A:H.464 pi-Stacking: B:F.201, B:F.201

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

DMS.2: 7 residues within 4Å: Chain A: L.76, S.79, A.80, W.84, E.85, F.86, G.88 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.86 pi-Cation interactions: A:F.86 DMS.3: 6 residues within 4Å: Chain A: Y.224, N.226, N.227, L.228, R.231, R.238 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.238 Water bridges: A:E.235 DMS.4: 3 residues within 4Å: Chain A: Q.40, S.42, P.45 1 PLIP interactions: 1 interactions with chain A Water bridges: A:T.41 DMS.5: 2 residues within 4Å: Chain A: G.232, F.233 1 PLIP interactions: 1 interactions with chain A pi-Cation interactions: A:F.233 DMS.6: 4 residues within 4Å: Chain A: R.77, A.247, N.248, Y.411 No protein-ligand interaction detected (PLIP) DMS.7: 3 residues within 4Å: Chain A: A.386, K.387, K.483 No protein-ligand interaction detected (PLIP) DMS.8: 4 residues within 4Å: Chain A: T.41, S.42, K.111, E.114 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.42 Salt bridges: A:E.114 DMS.12: 7 residues within 4Å: Chain B: L.76, S.79, A.80, W.84, E.85, F.86, G.88 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:F.86 pi-Cation interactions: B:F.86 DMS.13: 4 residues within 4Å: Chain B: G.300, N.301, V.302, G.303 No protein-ligand interaction detected (PLIP) DMS.14: 4 residues within 4Å: Chain B: Q.40, S.42, P.45, P.46 No protein-ligand interaction detected (PLIP) DMS.15: 5 residues within 4Å: Chain B: L.20, E.21, W.24, Y.113, M.116 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:E.21 pi-Cation interactions: B:W.24

2 x NUY: [4-(propan-2-yl)piperazin-1-yl](thiophen-2-yl)methanone(Non-covalent)

NUY.9: 3 residues within 4Å: Chain A: F.399, E.470, S.473 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:E.470 NUY.16: 3 residues within 4Å: Chain B: F.399, E.470, S.473 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:F.399 Water bridges: B:L.402 Salt bridges: B:E.470

2 x MG: MAGNESIUM ION(Non-covalent)

MG.10: 5 residues within 4Å: Chain A: F.117, N.118, T.120, L.123, D.124 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:F.117, A:T.120, A:L.123, H2O.1, H2O.7 MG.18: 3 residues within 4Å: Chain B: F.117, T.120, L.123 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:F.117, B:T.120, B:L.123, H2O.15, H2O.16

1 x BR: BROMIDE ION(Non-covalent)

BR.17: 5 residues within 4Å: Chain B: N.226, N.227, L.228, R.231, R.238 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fiorillo, A. et al., Innovative Approach for a Classic Target: Fragment Screening on Trypanothione Reductase Reveals New Opportunities for Drug Design. Front Mol Biosci (2022)

Release Date

2022-06-15

Peptides

N(1),N(8)-bis(glutathionyl)spermidine reductase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

N(1),N(8)-bis(glutathionyl)spermidine reductase

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