SMTL ID : 5lpo.1

tRNA guanine Transglycosylase (TGT) in co-crystallized complex with 6-amino-2-(methylamino)-4-(2-((2R,3R,4R,5R)-3,4,5-trimethoxytetrahydrofuran-2-yl)ethyl)-1H-imidazo[4,5-g]quinazolin-8(7H)-one

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.42 Å

Oligo State

homo-dimer

Ligands

10 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 9 residues within 4Å: Chain A: G.48, A.51, T.52, V.53, M.95, W.97 Chain B: W.328, Y.332, L.343 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:V.53, B:Y.332 GOL.2: 4 residues within 4Å: Chain A: P.254, D.256, K.257 Ligands: PG4.9 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.256, A:K.257 GOL.3: 8 residues within 4Å: Chain A: A.21, T.29, G.30, T.31, R.40, T.41, R.364 Ligands: GOL.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.30, A:T.41 GOL.4: 6 residues within 4Å: Chain A: R.40, Q.361, R.364, D.365, S.368 Ligands: GOL.3 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Q.361, A:R.364, A:D.365, A:S.368, A:S.368 Water bridges: A:R.40 GOL.5: 3 residues within 4Å: Chain A: S.190, R.191, K.192 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.192 Water bridges: A:E.193 GOL.10: 9 residues within 4Å: Chain A: W.328, Y.332, L.343 Chain B: G.48, A.51, T.52, V.53, M.95, W.97 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:V.53 GOL.11: 4 residues within 4Å: Chain B: P.254, D.256, K.257 Ligands: PG4.18 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.256, B:K.257 GOL.12: 8 residues within 4Å: Chain B: A.21, T.29, G.30, T.31, R.40, T.41, R.364 Ligands: GOL.13 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.30, B:T.41 GOL.13: 6 residues within 4Å: Chain B: R.40, Q.361, R.364, D.365, S.368 Ligands: GOL.12 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Q.361, B:R.364, B:D.365, B:S.368, B:S.368 Water bridges: B:R.40 GOL.14: 3 residues within 4Å: Chain B: S.190, R.191, K.192 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.192 Water bridges: B:E.193

2 x ZN: ZINC ION(Non-covalent)

ZN.6: 4 residues within 4Å: Chain A: C.320, C.322, C.325, H.351 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.320, A:C.322, A:C.325, A:H.351 ZN.15: 4 residues within 4Å: Chain B: C.320, C.322, C.325, H.351 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.320, B:C.322, B:C.325, B:H.351

2 x 725: 6-amino-2-(methylamino)-4-(2-((2R,3R,4R,5R)-3,4,5-trimethoxytetrahydrofuran-2-yl)ethyl)-1H-imidazo[4,5-g]quinazolin-8(7H)-one(Non-covalent)

725.7: 18 residues within 4Å: Chain A: L.70, L.102, D.104, S.105, Y.108, D.158, C.160, I.203, Q.205, G.231, G.232, L.233, A.234, V.235, Y.260, M.262, G.263, D.282 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:Y.108, A:M.262 Hydrogen bonds: A:D.104, A:S.105, A:Q.205, A:G.232, A:A.234 Water bridges: A:D.158, A:C.160, A:V.284 Salt bridges: A:D.104, A:D.158 pi-Stacking: A:Y.108, A:Y.108 725.16: 18 residues within 4Å: Chain B: L.70, L.102, D.104, S.105, Y.108, D.158, C.160, I.203, Q.205, G.231, G.232, L.233, A.234, V.235, Y.260, M.262, G.263, D.282 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:Y.108, B:M.262 Hydrogen bonds: B:D.104, B:D.104, B:S.105, B:Q.205, B:G.232, B:A.234 Water bridges: B:D.158, B:C.160, B:D.282, B:V.284 Salt bridges: B:D.104, B:D.158 pi-Stacking: B:Y.108, B:Y.108

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

EDO.8: 4 residues within 4Å: Chain A: H.147, G.150, S.151, N.197 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.147 Water bridges: A:Q.194 EDO.17: 4 residues within 4Å: Chain B: H.147, G.150, S.151, N.197 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.147, B:H.147 Water bridges: B:Q.194

2 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.9: 7 residues within 4Å: Chain A: S.17, F.18, S.19, I.20, D.256, K.257 Ligands: GOL.2 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:D.256 Hydrogen bonds: A:F.18, A:I.20, A:I.20 PG4.18: 7 residues within 4Å: Chain B: S.17, F.18, S.19, I.20, D.256, K.257 Ligands: GOL.11 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:D.256 Hydrogen bonds: B:F.18, B:I.20, B:I.20

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ehrmann, F.R. et al., Carbohydrate-based Inhibitors targeting the Ribose-34 pocket of Z.mobilis TGT and changing the oligomeric state of the homodimer. To be published

Release Date

2017-08-30

Peptides

Queuine tRNA-ribosyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Queuine tRNA-ribosyltransferase

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