SMTL ID : 9ife.1 (1 other biounit)

PANDDA analysis - Crystal structure of Trypanosoma brucei trypanothione reductase in complex with Z943693514

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.68 Å

Oligo State

homo-dimer

Ligands

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

FAD.1: 38 residues within 4Å: Chain A: 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, 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 34 PLIP interactions: 32 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:T.54, A:I.202, A:I.202 Hydrogen bonds: A:S.17, A:S.17, A:G.18, A:G.19, A:V.39, A:A.49, A:G.53, A:T.54, A:C.55, A:K.63, A:G.130, A:G.130, A:R.293, A:D.330, A:M.336, A:T.338, A:T.338, A:T.338, B:H.464 Water bridges: A:G.16, A:S.17, A:A.49, A:G.52, A:T.54, A:G.164, A:G.164, A:S.165, A:A.341, B:H.464 pi-Stacking: A:F.201, A:F.201 FAD.9: 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 32 PLIP interactions: 30 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:V.39, B:A.49, B:G.53, B:T.54, B:T.54, B:C.55, B:K.63, B:G.130, B:G.130, B:G.164, B:R.293, B:D.330, B:M.336, B:T.338, B:T.338, A:H.464 Water bridges: B:G.16, B:S.17, B:A.49, B:G.52, B:S.165, B:S.165, B:I.331, A:H.464 pi-Stacking: B:F.201, B:F.201

3 x IMD: IMIDAZOLE(Non-covalent)

IMD.2: 4 residues within 4Å: Chain A: A.80, W.84, E.85, F.86 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.86 IMD.5: 6 residues within 4Å: Chain A: H.362, T.363, R.364, V.365, C.378, G.379 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.364, A:V.365, A:G.379 IMD.10: 4 residues within 4Å: Chain B: A.80, W.84, E.85, F.86 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:F.86, B:G.88 Water bridges: B:F.86

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

PEG.3: 6 residues within 4Å: Chain A: W.166, P.167, M.169, C.178, S.180, E.183 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:P.167 Water bridges: A:S.180 PEG.4: 5 residues within 4Å: Chain A: L.299, G.300, G.303, V.304, L.306 2 PLIP interactions: 2 interactions with chain A Water bridges: A:T.294, A:Q.298 PEG.11: 10 residues within 4Å: Chain B: P.167, G.200, F.201, I.202, M.286, A.287, I.288, G.289, R.290 Ligands: PEG.12 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:I.202, B:G.289 Water bridges: B:S.181, B:S.203, B:M.286, B:I.288 PEG.12: 10 residues within 4Å: Chain B: G.198, G.199, G.200, Y.224, R.225, A.287, I.288, G.289 Ligands: PEG.11, NA.14 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.199, B:G.200 Water bridges: B:R.225, B:R.225

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

DMS.6: 5 residues within 4Å: Chain A: Q.40, S.42, H.43, P.45, P.46 No protein-ligand interaction detected (PLIP)

3 x BR: BROMIDE ION(Non-covalent)

BR.7: 4 residues within 4Å: Chain A: N.94, W.95, K.96, P.190 Ligand excluded by PLIP BR.8: 3 residues within 4Å: Chain A: S.455, Y.458, R.475 Ligand excluded by PLIP BR.13: 5 residues within 4Å: Chain B: N.226, N.227, L.228, R.231, R.238 Ligand excluded by PLIP

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

NA.14: 5 residues within 4Å: Chain B: G.198, Y.224, R.225, I.288 Ligands: PEG.12 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.225 Water bridges: B:C.223, B:R.225, B:R.225, B:N.257

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Exertier, C. et al., Expanding the molecular landscape of fragments binding to trypanothione reductase, a legitimate target for drug design against human African trypanosomiasis. Front Chem Biol (2025)

Release Date

2025-11-12

Peptides

Trypanothione reductase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Trypanothione reductase

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