SMTL ID : 9ifl.2 (1 other biounit)

PANDDA analysis - Crystal structure of Trypanosoma brucei trypanothione reductase in complex with Z319545618

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.71 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 33 PLIP interactions: 31 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:A.50, A:G.53, 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:S.17, A:A.49, A:G.52, A:S.165, A:I.331, A:A.341, B:H.464 pi-Stacking: A:F.201, A:F.201 FAD.7: 38 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, S.181, F.201, I.202, R.290, R.293, G.329, D.330, M.336, L.337, T.338, P.339, A.341 34 PLIP interactions: 32 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:A.50, B:G.53, 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:T.54, B:S.165, B:S.165, B:I.331, B:A.341, 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 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:F.86, A:G.88 Water bridges: A:F.86 IMD.6: 5 residues within 4Å: Chain A: I.291, P.292, R.293, T.294, N.295 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.295 Water bridges: A:R.293 IMD.8: 4 residues within 4Å: Chain B: R.77, A.247, N.248, Y.411 No protein-ligand interaction detected (PLIP)

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

PEG.3: 4 residues within 4Å: Chain A: W.166, M.169, S.180, E.183 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:W.166, A:S.180 Water bridges: A:C.178, A:N.182 PEG.4: 4 residues within 4Å: Chain A: A.386, K.387, K.483, G.484 No protein-ligand interaction detected (PLIP) PEG.9: 6 residues within 4Å: Chain B: W.166, M.169, I.175, C.178, S.180, E.183 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:I.175, B:S.180 Water bridges: B:N.182

2 x RXS: 3-[(2-methyl-1H-imidazol-1-yl)methyl]benzonitrile(Non-covalent)

RXS.5: 9 residues within 4Å: Chain A: L.20, E.21, G.23, W.24, V.36, Y.113, M.116, F.117, L.123 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:L.20, A:L.20, A:W.24, A:W.24, A:Y.113, A:Y.113, A:M.116, A:F.117, A:L.123 pi-Stacking: A:W.24 RXS.10: 9 residues within 4Å: Chain B: L.20, E.21, G.23, W.24, V.36, Y.113, M.116, F.117, L.123 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:L.20, B:L.20, B:W.24, B:W.24, B:Y.113, B:M.116, B:F.117, B:L.123

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

NA.11: 3 residues within 4Å: Chain B: G.198, Y.224, R.225 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.225 Water bridges: B:C.223, 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
C

B
D

Trypanothione reductase

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