SMTL ID : 2yau.1

X-ray structure of the Leishmania infantum tryopanothione reductase in complex with auranofin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.50 Å

Oligo State

homo-dimer

Ligands

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

FAD.1: 36 residues within 4Å: Chain A: G.31, G.33, S.34, G.35, G.36, V.54, D.55, V.56, A.66, A.67, G.70, T.71, C.72, V.75, G.76, C.77, K.80, G.145, F.146, G.147, A.179, T.180, G.181, S.198, R.307, R.310, G.346, D.347, M.353, L.354, T.355, P.356, A.358 Chain B: H.481, P.482 Ligands: NDP.2 21 PLIP interactions: 19 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:S.34, A:S.34, A:G.35, A:G.36, A:V.56, A:A.66, A:A.67, A:T.71, A:T.71, A:T.71, A:T.71, A:C.72, A:K.80, A:G.147, A:G.147, A:D.347, A:M.353, A:T.355, A:T.355, B:H.481, B:H.481 FAD.7: 37 residues within 4Å: Chain A: H.481, P.482 Chain B: G.31, G.33, S.34, G.35, G.36, V.54, D.55, V.56, A.66, A.67, G.70, T.71, C.72, V.75, G.76, C.77, K.80, G.145, F.146, G.147, A.179, T.180, G.181, S.198, R.307, R.310, I.345, G.346, D.347, M.353, L.354, T.355, P.356, A.358 Ligands: NDP.8 20 PLIP interactions: 18 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:S.34, B:S.34, B:G.35, B:G.36, B:A.66, B:G.70, B:T.71, B:T.71, B:C.72, B:K.80, B:G.147, B:G.147, B:R.310, B:D.347, B:M.353, B:T.355, B:T.355, B:T.355, A:H.481, A:H.481

2 x NDP: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NDP.2: 19 residues within 4Å: Chain A: K.80, G.216, G.217, Y.218, I.219, E.222, Y.241, R.242, R.248, N.274, A.304, I.305, G.306, R.307, M.353, L.354, A.385, F.387 Ligands: FAD.1 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:Y.218, A:Y.218, A:I.219 Hydrogen bonds: A:K.80, A:G.216, A:G.216, A:G.217, A:I.219, A:Y.241, A:Y.241, A:N.274, A:A.385 Salt bridges: A:R.242 pi-Cation interactions: A:R.242, A:R.242 NDP.8: 19 residues within 4Å: Chain B: K.80, G.216, G.217, Y.218, I.219, E.222, Y.241, R.242, R.248, N.274, A.304, I.305, G.306, R.307, M.353, L.354, A.385, F.387 Ligands: FAD.7 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:Y.218, B:Y.218, B:I.219 Hydrogen bonds: B:K.80, B:G.216, B:G.216, B:Y.218, B:I.219, B:Y.241, B:N.274, B:A.385 Salt bridges: B:R.242 pi-Cation interactions: B:R.242, B:R.242

2 x AU: GOLD ION(Non-covalent)

AU.3: 5 residues within 4Å: Chain A: C.72, C.77, T.355 Chain B: H.481 Ligands: CL.5 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:C.72, A:C.77 AU.9: 5 residues within 4Å: Chain A: H.481 Chain B: C.72, C.77, T.355 Ligands: CL.11 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:C.72, B:C.77

2 x TS8: 2,3,4,6-tetra-O-acetyl-1-thio-beta-D-glucopyranose(Non-covalent)

TS8.4: 9 residues within 4Å: Chain B: F.416, L.419, H.481, P.482, T.483, E.486, E.487 Ligands: CL.5, SO4.12 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:F.416, B:L.419 Hydrogen bonds: B:T.483, B:E.486 Salt bridges: B:H.481, B:H.481 TS8.10: 9 residues within 4Å: Chain A: F.416, T.417, L.419, H.481, P.482, E.486, E.487 Ligands: SO4.6, CL.11 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.416, A:L.419 Salt bridges: A:H.481, A:H.481

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.5: 7 residues within 4Å: Chain A: S.34, C.72, V.73, C.77 Chain B: H.481 Ligands: AU.3, TS8.4 Ligand excluded by PLIP CL.11: 6 residues within 4Å: Chain B: S.34, C.72, V.73, T.355 Ligands: AU.9, TS8.10 Ligand excluded by PLIP

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.6: 7 residues within 4Å: Chain A: P.418, L.419, P.482, T.483, S.484 Chain B: K.81 Ligands: TS8.10 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:L.419, A:S.484 Salt bridges: B:K.81 SO4.12: 8 residues within 4Å: Chain A: K.81 Chain B: F.416, P.418, L.419, P.482, T.483, S.484 Ligands: TS8.4 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:L.419 Salt bridges: A:K.81

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ilari, A. et al., A Gold-Containing Drug Against Parasitic Polyamine Metabolism: The X-Ray Structure of Trypanothione Reductase from Leishmania Infantum in Complex with Auranofin Reveals a Dual Mechanism of Enzyme Inhibition. Amino Acids (2012)

Release Date

2012-01-11

Peptides

TRYPANOTHIONE REDUCTASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

TRYPANOTHIONE REDUCTASE

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