SMTL ID : 8ccl.1

Crystal structure of Mycobacterium smegmatis thioredoxin reductase in complex with fragment F2X-Entry A09

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-dimer

Ligands

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

FAD.1: 39 residues within 4Å: Chain A: I.21, G.22, S.23, G.24, P.25, A.26, F.44, E.45, G.46, Q.48, F.49, G.50, G.51, A.52, L.53, T.55, T.56, V.59, N.61, E.92, D.93, V.94, A.121, M.122, G.123, A.124, T.144, C.148, R.253, L.256, G.287, D.288, R.295, Q.296, A.297, A.300 Chain B: Y.33 Ligands: MG.6, MG.7 26 PLIP interactions: 26 interactions with chain A Hydrophobic interactions: A:A.52 Hydrogen bonds: A:S.23, A:G.24, A:A.26, A:G.51, A:A.52, A:N.61, A:N.61, A:V.94, A:V.94, A:A.124, A:R.253, A:D.288, A:R.295, A:A.297 Water bridges: A:G.27, A:Q.48, A:G.50, A:L.53, A:T.56, A:N.61, A:R.253, A:D.288, A:L.289, A:L.289, A:I.298 FAD.8: 39 residues within 4Å: Chain A: Y.33 Chain B: I.21, G.22, S.23, G.24, P.25, A.26, F.44, E.45, G.46, Q.48, F.49, G.50, G.51, A.52, L.53, T.55, T.56, V.59, N.61, E.92, D.93, V.94, A.121, M.122, G.123, A.124, T.144, C.148, R.253, L.256, G.287, D.288, R.295, Q.296, A.297, A.300 Ligands: MG.13, MG.14 25 PLIP interactions: 24 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:A.52 Hydrogen bonds: B:S.23, B:G.24, B:A.26, B:G.51, B:A.52, B:N.61, B:N.61, B:V.94, B:V.94, B:A.124, B:R.253, B:D.288, B:R.295, B:A.297, A:Y.33 Water bridges: B:G.27, B:Q.48, B:G.50, B:L.53, B:N.61, B:R.253, B:L.289, B:L.289, B:I.298

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 6 residues within 4Å: Chain A: M.54, T.55, T.56, T.57, T.138, G.139 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:M.54, A:T.57, A:T.138 GOL.9: 6 residues within 4Å: Chain B: M.54, T.55, T.56, T.57, T.138, G.139 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:M.54, B:T.57, B:T.138

4 x MLI: MALONATE ION(Non-functional Binders)

MLI.3: 3 residues within 4Å: Chain A: D.95, E.255, L.256 No protein-ligand interaction detected (PLIP) MLI.4: 7 residues within 4Å: Chain A: E.262, K.270, V.271, Q.272, Y.277, T.278, S.279 1 PLIP interactions: 1 interactions with chain A Water bridges: A:G.273 MLI.10: 3 residues within 4Å: Chain B: D.95, E.255, L.256 No protein-ligand interaction detected (PLIP) MLI.11: 7 residues within 4Å: Chain B: E.262, K.270, V.271, Q.272, Y.277, T.278, S.279 1 PLIP interactions: 1 interactions with chain B Water bridges: B:G.273

2 x U8O: [1,2]thiazolo[5,4-b]pyridin-3-amine(Non-covalent)

U8O.5: 7 residues within 4Å: Chain A: L.129, V.131, V.161, R.186, E.213, I.214, I.248 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.129, A:I.248 Hydrogen bonds: A:L.129, A:I.214 U8O.12: 7 residues within 4Å: Chain B: L.129, V.131, V.161, R.186, E.213, I.214, I.248 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:L.129, B:I.248 Hydrogen bonds: B:L.129, B:I.214

4 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.6: 3 residues within 4Å: Chain A: G.51, A.52 Ligands: FAD.1 No protein-ligand interaction detected (PLIP) MG.7: 1 residues within 4Å: Ligands: FAD.1 No protein-ligand interaction detected (PLIP) MG.13: 3 residues within 4Å: Chain B: G.51, A.52 Ligands: FAD.8 No protein-ligand interaction detected (PLIP) MG.14: 1 residues within 4Å: Ligands: FAD.8 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fuesser, F.T. et al., Fragment-based design of mycobacterial thioredoxin reductase inhibitors based on computational exploration of a huge virtual space. To Be Published

Release Date

2024-02-07

Peptides

Thioredoxin reductase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Thioredoxin reductase

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