SMTL ID : 5jgm.1

tRNA guanine Transglycosylase (TGT) in co-crystallized complex with ethyl (2-(methylamino)-8-oxo-7,8-dihydro-1H-imidazo[4,5-g]quinazolin-6-yl)carbamate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.38 Å

Oligo State

homo-dimer

Ligands

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 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.2: 4 residues within 4Å: Chain A: K.52 Chain B: G.338, E.339, I.340 7 PLIP interactions: 3 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:R.289, B:I.340 Water bridges: A:K.52, A:K.52, B:G.338, B:E.339, B:L.341 GOL.3: 7 residues within 4Å: Chain A: W.296, E.317, K.360, F.373, D.376, F.377, R.380 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.317, A:K.360, A:D.376, A:R.380 Water bridges: A:E.317 GOL.10: 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.11: 4 residues within 4Å: Chain A: G.338, E.339, I.340 Chain B: K.52 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:I.340, B:R.289 Water bridges: A:G.338, A:E.339, A:E.339, B:K.52, B:K.52 GOL.12: 7 residues within 4Å: Chain B: W.296, E.317, K.360, F.373, D.376, F.377, R.380 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:E.317, B:K.360, 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.13: 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

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

EDO.5: 5 residues within 4Å: Chain A: R.34, H.145, G.148, S.149, Q.192 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.34, A:H.145 Water bridges: A:Q.192, A:N.195 EDO.6: 5 residues within 4Å: Chain A: V.206, F.207, E.208, R.242, F.246 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:V.206, A:E.208, A:R.242, A:R.242 Water bridges: A:N.209 EDO.7: 3 residues within 4Å: Chain A: P.162, A.163, T.164 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:P.162, A:T.164 EDO.14: 5 residues within 4Å: Chain B: R.34, H.145, G.148, S.149, Q.192 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.34, B:H.145, B:H.145 Water bridges: B:Q.192, B:N.195 EDO.15: 5 residues within 4Å: Chain B: V.206, F.207, E.208, R.242, F.246 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:V.206, B:E.208, B:R.242, B:R.242 Water bridges: B:N.209 EDO.16: 3 residues within 4Å: Chain B: P.162, A.163, T.164 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:P.162, B:T.164

2 x 810: ethyl [2-(methylamino)-8-oxo-7,8-dihydro-1H-imidazo[4,5-g]quinazolin-6-yl]carbamate(Non-covalent)

810.8: 18 residues within 4Å: Chain A: D.102, S.103, Y.106, M.153, A.154, D.156, C.158, I.201, Q.203, G.229, G.230, L.231, A.232, V.233, Y.258, M.260, G.261 Ligands: CL.9 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:D.102, A:Y.258, A:M.260 Hydrogen bonds: A:S.103, A:D.156, A:D.156, A:Q.203, A:G.230, A:L.231, A:A.232 pi-Stacking: A:Y.106, A:Y.106 810.17: 18 residues within 4Å: Chain B: D.102, S.103, Y.106, M.153, A.154, D.156, C.158, I.201, Q.203, G.229, G.230, L.231, A.232, V.233, Y.258, M.260, G.261 Ligands: CL.18 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:D.102, B:Y.258, B:M.260 Hydrogen bonds: B:S.103, B:D.156, B:D.156, B:Q.203, B:G.230, B:L.231, B:A.232 pi-Stacking: B:Y.106, B:Y.106

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

CL.9: 4 residues within 4Å: Chain A: G.261, C.281, V.282 Ligands: 810.8 Ligand excluded by PLIP CL.18: 4 residues within 4Å: Chain B: G.261, C.281, V.282 Ligands: 810.17 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ehrmann, F.R. et al., Carbamate-protected lin-Benzoguanines as promising candidates for improving solubility and membrane permeability. To be Published

Release Date

2017-05-10

Peptides

Queuine tRNA-ribosyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Queuine tRNA-ribosyltransferase

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