SMTL ID : 5j9m.1

tRNA guanine Transglycosylase (TGT) in co-crystallized complex with 2-(methylamino)-1H-benzo[d]imidazole-5-carboxamide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.33 Å

Oligo State

homo-dimer

Ligands

2 x 6HD: 2-(methylamino)-1H-benzimidazole-5-carboxamide(Non-covalent)

6HD.1: 11 residues within 4Å: Chain A: Y.106, D.156, C.158, Q.203, G.229, G.230, L.231, A.232, V.233, M.260, G.261 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:Y.106, A:M.260 Hydrogen bonds: A:D.156, A:Q.203, A:G.230, A:A.232 pi-Stacking: A:Y.106, A:Y.106 6HD.7: 11 residues within 4Å: Chain B: Y.106, D.156, C.158, Q.203, G.229, G.230, L.231, A.232, V.233, M.260, G.261 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:Y.106, B:M.260 Hydrogen bonds: B:D.156, B:Q.203, B:G.230, B:A.232 pi-Stacking: B:Y.106, B:Y.106

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 6 residues within 4Å: Chain A: P.56, E.57, G.94, W.95, D.96, R.97 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:P.56, A:D.96, A:D.96, A:R.97 Water bridges: A:E.57, A:R.97 GOL.3: 7 residues within 4Å: Chain A: W.296, E.317, K.360, F.373, D.376, F.377, R.380 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.317, A:D.376, A:R.380 Water bridges: A:E.317 GOL.8: 6 residues within 4Å: Chain B: P.56, E.57, G.94, W.95, D.96, R.97 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:P.56, B:D.96, B:D.96, B:R.97 Water bridges: B:E.57, B:R.97 GOL.9: 7 residues within 4Å: Chain B: W.296, E.317, K.360, F.373, D.376, F.377, R.380 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.317, B:D.376, B:R.380 Water bridges: B:K.360

2 x ZN: ZINC ION(Non-covalent)

ZN.4: 4 residues within 4Å: Chain A: C.318, C.320, C.323, H.349 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.318, A:C.320, A:C.323, A:H.349 ZN.10: 4 residues within 4Å: Chain B: C.318, C.320, C.323, H.349 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.318, B:C.320, B:C.323, B:H.349

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.5: 4 residues within 4Å: Chain A: H.145, G.148, S.149, Q.192 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.145 Water bridges: A:D.150, A:Q.192 EDO.11: 4 residues within 4Å: Chain B: H.145, G.148, S.149, Q.192 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:H.145, B:H.145 Water bridges: B:D.150, B:Q.192

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

CL.6: 5 residues within 4Å: Chain A: K.52, V.282, T.285, R.286, R.289 Ligand excluded by PLIP CL.12: 5 residues within 4Å: Chain B: K.52, V.282, T.285, R.286, R.289 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ehrmann, F.R. et al., Benzimidazole-based Inhibitors as a Novel Scaffold to Inhibit Z.mobilis TGT and Study Protein Flexibility and the Contributions of Active Site Residues to Binding Affinity of lin-Benzopurines. To be Published

Release Date

2017-05-24

Peptides

Queuine tRNA-ribosyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Queuine tRNA-ribosyltransferase

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