SMTL ID : 4cbq.1

Crystal structure of the thioredoxin reductase from Entamoeba histolytica with auranofin Au(I) bound to Cys286

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.94 Å

Oligo State

homo-dimer

Ligands

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

NDP.1: 13 residues within 4Å: Chain A: G.160, G.161, D.162, A.163, E.166, H.182, R.183, R.184, R.188, A.245, I.246 Ligands: SO4.2, FAD.6 22 PLIP interactions: 22 interactions with chain A Hydrogen bonds: A:G.160, A:G.160, A:D.162, A:A.163, A:E.166, A:R.183 Water bridges: A:G.159, A:G.161, A:D.162, A:D.162, A:A.164, A:R.183, A:R.183, A:R.183, A:G.247, A:H.248 Salt bridges: A:H.182, A:R.183, A:R.184, A:R.188 pi-Cation interactions: A:R.183, A:R.183 NDP.7: 17 residues within 4Å: Chain A: L.305 Chain B: K.122, G.160, G.161, D.162, A.163, H.182, R.183, R.184, R.188, A.245, I.246, H.248, V.289, Y.290, R.291, Q.292 26 PLIP interactions: 26 interactions with chain B Hydrogen bonds: B:K.122, B:G.160, B:G.160, B:D.162, B:D.162, B:D.162, B:A.163, B:R.291, B:Q.292 Water bridges: B:G.161, B:A.164, B:H.182, B:R.183, B:R.184, B:R.188, B:G.247, B:G.247 Salt bridges: B:H.182, B:R.183, B:R.188, B:R.188, B:H.248, B:R.291, B:R.291 pi-Cation interactions: B:R.183, B:R.183

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

SO4.2: 2 residues within 4Å: Chain A: R.183 Ligands: NDP.1 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.183 SO4.3: 5 residues within 4Å: Chain A: P.127, G.128, E.129, D.130, K.131 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.128, A:D.130, A:D.130, A:K.131 Water bridges: A:E.129, A:E.129 SO4.4: 6 residues within 4Å: Chain A: L.268, T.269, E.270, K.273, T.274, S.275 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.273 Water bridges: A:L.268 SO4.8: 6 residues within 4Å: Chain B: K.260, L.268, T.269, K.273, T.274, S.275 1 PLIP interactions: 1 interactions with chain B Water bridges: B:L.268 SO4.9: 5 residues within 4Å: Chain B: P.127, G.128, E.129, D.130, K.131 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:G.128, B:D.130, B:D.130, B:K.131 Water bridges: B:E.129, B:E.129

2 x AU: GOLD ION(Non-covalent)

AU.5: 2 residues within 4Å: Chain A: G.283, C.286 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:C.286 AU.10: 4 residues within 4Å: Chain B: G.283, C.286, D.287 Ligands: CL.11 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:C.286

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

FAD.6: 36 residues within 4Å: Chain A: I.10, G.11, S.12, G.13, P.14, A.15, Y.33, E.34, G.35, A.38, V.41, A.42, A.43, G.45, Q.46, L.47, T.49, T.50, I.53, N.55, E.86, T.87, I.88, A.116, T.117, G.118, A.119, H.248, G.283, D.284, R.291, Q.292, A.293, A.296 Chain B: Y.22 Ligands: NDP.1 25 PLIP interactions: 24 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.12, A:A.15, A:V.41, A:Q.46, A:N.55, A:N.55, A:I.88, A:I.88, A:A.119, A:A.119, A:D.284, A:R.291, A:Q.292, A:A.293, B:Y.22 Water bridges: A:G.13, A:G.13, A:L.47, A:L.47, A:T.50, A:N.55, A:D.89, A:G.118, A:V.285, A:I.294 FAD.13: 34 residues within 4Å: Chain A: Y.22 Chain B: I.10, G.11, S.12, G.13, P.14, A.15, Y.33, E.34, G.35, A.38, V.41, A.42, A.43, G.45, Q.46, L.47, T.49, T.50, I.53, N.55, E.86, T.87, I.88, A.116, T.117, G.118, A.119, G.283, D.284, R.291, Q.292, A.293, A.296 27 PLIP interactions: 26 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:Q.46, B:T.50 Hydrogen bonds: B:S.12, B:A.15, B:A.42, B:G.45, B:Q.46, B:Q.46, B:N.55, B:N.55, B:I.88, B:I.88, B:A.119, B:D.284, B:R.291, B:A.293, A:Y.22 Water bridges: B:G.13, B:G.13, B:L.47, B:L.47, B:T.50, B:N.55, B:G.118, B:D.284, B:Q.292, B:I.294

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

CL.11: 3 residues within 4Å: Chain B: D.287, V.295 Ligands: AU.10 Ligand excluded by PLIP CL.12: 4 residues within 4Å: Chain A: G.298 Chain B: V.295, G.298, S.299 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Parsonage, D. et al., X-Ray Structures of Thioredoxin and Thioredoxin Reductase from Entamoeba Histolytica and Prevailing Hypothesis of the Mechanism of Auranofin Action. J.Struct.Biol. (2016)

Release Date

2014-11-05

Peptides

THIOREDOXIN REDUCTASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

THIOREDOXIN REDUCTASE

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