SMTL ID : 5jsv.1

tRNA guanine Transglycosylase (TGT) in co-crystallized complex with 6-amino-2-((((3aR,4R,6R,6aR)-6-methoxy-2,2-dimethyltetrahydrofuro[3,4-d][1,3]dioxol-4-yl)methyl)amino)-1H-imidazo[4,5-g]quinazolin-8(7H)-one

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.17 Å

Oligo State

homo-dimer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 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.7: 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 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.4: 5 residues within 4Å: Chain A: C.323, Q.324, K.325, W.326, S.327 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:C.323, A:K.325 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 GOL.10: 5 residues within 4Å: Chain B: C.323, Q.324, K.325, W.326, S.327 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:C.323, B:K.325

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

CL.5: 4 residues within 4Å: Chain A: V.282, T.285, R.286, R.289 Ligand excluded by PLIP CL.11: 4 residues within 4Å: Chain B: V.282, T.285, R.286, R.289 Ligand excluded by PLIP

2 x 6MQ: methyl 5-[(6-amino-8-oxo-7,8-dihydro-3H-imidazo[4,5-g]quinazolin-2-yl)amino]-5-deoxy-2,3-O-(1-methylethylidene)-beta-D-ribofuranoside(Non-covalent)

6MQ.6: 15 residues within 4Å: Chain A: D.102, S.103, G.105, Y.106, D.156, C.158, I.201, Q.203, G.229, G.230, L.231, A.232, M.260, G.261, V.282 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:M.260 Hydrogen bonds: A:S.103, A:G.105, A:Y.106, A:Y.106, A:Q.203, A:G.230, A:A.232 Water bridges: A:G.104, A:L.231, A:D.280, A:R.286, A:R.286, A:R.286 Salt bridges: A:D.102, A:D.156, A:R.286 6MQ.12: 15 residues within 4Å: Chain B: D.102, S.103, G.105, Y.106, D.156, C.158, I.201, Q.203, G.229, G.230, L.231, A.232, M.260, G.261, V.282 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:M.260 Hydrogen bonds: B:S.103, B:G.105, B:Y.106, B:Q.203, B:G.230, B:A.232 Water bridges: B:G.104, B:L.231, B:D.280, B:R.286, B:R.286, B:R.286 Salt bridges: B:D.102, B:D.156, B:R.286

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ehrmann, F.R. et al., Application of carbohydrates based lin-benzoguanines in a solvent-exposed subpocket of the tRNA-modifying Enzyme TGT. 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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