SMTL ID : 6fmn.1

tRNA guanine Transglycosylase (TGT) in co-crystallized complex with 6-amino-2-((((2R,3S,4R,5R)-3,4-dihydroxy-5-methoxytetrahydrofuran-2-yl)methyl)amino)-1,7-dihydro-8H-imidazo[4,5-g]quinazolin-8-one

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.36 Å

Oligo State

homo-dimer

Ligands

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 8 residues within 4Å: Chain A: P.56, E.57, R.60, G.94, W.95, D.96, R.97 Chain B: K.325 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:P.56, A:G.94, A:D.96, A:R.97, B:K.325 Water bridges: A:E.57, A:R.97 GOL.2: 5 residues within 4Å: Chain A: A.305, S.308, H.332, R.336 Chain B: R.82 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:R.82, B:R.82, A:H.332 Water bridges: A:S.308, A:R.336, A:R.336 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.7: 8 residues within 4Å: Chain A: K.325 Chain B: P.56, E.57, R.60, G.94, W.95, D.96, R.97 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:P.56, B:G.94, B:D.96, B:R.97, A:K.325 Water bridges: B:E.57, B:R.97 GOL.8: 5 residues within 4Å: Chain A: R.82 Chain B: A.305, S.308, H.332, R.336 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:H.332, A:R.82, A:R.82 Water bridges: B:S.308, B:R.336, B:R.336 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:K.360, B:D.376, B:R.380

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

CL.4: 5 residues within 4Å: Chain A: K.52, V.282, T.285, R.286, R.289 Ligand excluded by PLIP CL.10: 5 residues within 4Å: Chain B: K.52, V.282, T.285, R.286, R.289 Ligand excluded by PLIP

2 x ZN: ZINC ION(Non-covalent)

ZN.5: 5 residues within 4Å: Chain A: C.318, C.320, V.322, 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.11: 5 residues within 4Å: Chain B: C.318, C.320, V.322, 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 E4E: 6-azanyl-2-[[(2~{R},3~{S},4~{R},5~{R})-5-methoxy-3,4-bis(oxidanyl)oxolan-2-yl]methylamino]-3,7-dihydroimidazo[4,5-g]quinazolin-8-one(Non-covalent)

E4E.6: 16 residues within 4Å: Chain A: D.102, S.103, Y.106, D.156, C.158, I.201, Q.203, G.229, G.230, L.231, A.232, V.233, M.260, G.261, V.282, R.286 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:M.260 Hydrogen bonds: A:S.103, A:Q.203, A:G.230, A:A.232, A:A.232, A:R.286 Water bridges: A:D.102, A:Y.106, A:G.261 Salt bridges: A:D.102, A:D.156 pi-Stacking: A:Y.106, A:Y.106 E4E.12: 16 residues within 4Å: Chain B: D.102, S.103, Y.106, D.156, C.158, I.201, Q.203, G.229, G.230, L.231, A.232, V.233, M.260, G.261, V.282, R.286 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:M.260 Hydrogen bonds: B:S.103, B:Q.203, B:G.230, B:A.232, B:A.232, B:R.286 Water bridges: B:D.102, B:D.102, B:Y.106 Salt bridges: B:D.102, B:D.156 pi-Stacking: B:Y.106, B:Y.106

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Movsisyan, L.D. et al., Sugar Acetonides are a Superior Motif for Addressing the Large, Solvent-Exposed Ribose-33 Pocket of tRNA-Guanine Transglycosylase. Chemistry (2018)

Release Date

2019-03-13

Peptides

Queuine tRNA-ribosyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Queuine tRNA-ribosyltransferase

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