SMTL ID : 4q8w.1

tRNA-Guanine Transglycosylase (TGT) in Complex with 4-[2-({6-Amino-8-oxo-1H,7H,8H-imidazo[4,5-g]quinazolin-2-yl}amino)ethyl]benzoic acid

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.14 Å

Oligo State

homo-dimer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 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.7: 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 2YY: 4-{2-[(6-amino-8-oxo-7,8-dihydro-1H-imidazo[4,5-g]quinazolin-2-yl)amino]ethyl}benzoic acid(Non-covalent)

2YY.2: 17 residues within 4Å: Chain A: D.104, S.105, Y.108, D.158, C.160, I.203, Q.205, G.231, G.232, L.233, A.234, M.262, G.263, C.283, V.284, L.285, R.288 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:V.284 Hydrogen bonds: A:S.105, A:Q.205, A:G.232, A:L.233, A:A.234 Water bridges: A:L.233 Salt bridges: A:D.104, A:D.158, A:R.288 pi-Stacking: A:Y.108, A:Y.108 2YY.8: 17 residues within 4Å: Chain B: D.104, S.105, Y.108, D.158, C.160, I.203, Q.205, G.231, G.232, L.233, A.234, M.262, G.263, C.283, V.284, L.285, R.288 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:V.284 Hydrogen bonds: B:S.105, B:Q.205, B:G.232, B:L.233, B:A.234 Water bridges: B:D.104, B:Y.108, B:L.233 Salt bridges: B:D.104, B:D.158, B:R.288 pi-Stacking: B:Y.108, B:Y.108

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 7 residues within 4Å: Chain A: P.58, E.59, G.96, W.97, D.98, R.99 Chain B: K.327 6 PLIP interactions: 1 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:K.327, A:P.58, A:G.96, A:D.98, A:R.99 Water bridges: A:E.59 GOL.4: 7 residues within 4Å: Chain A: W.298, E.319, K.362, F.375, D.378, F.379, R.382 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.319, A:K.362, A:D.378, A:R.382 Water bridges: A:E.319 GOL.5: 7 residues within 4Å: Chain A: L.313, P.315, C.325, Q.326, K.327, W.328, S.329 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:L.313, A:C.325 Water bridges: B:S.93, B:S.93 GOL.6: 2 residues within 4Å: Chain A: A.22, R.23 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.23 GOL.9: 7 residues within 4Å: Chain A: K.327 Chain B: P.58, E.59, G.96, W.97, D.98, R.99 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:P.58, B:G.96, B:D.98, B:R.99, A:K.327 Water bridges: B:E.59 GOL.10: 7 residues within 4Å: Chain B: W.298, E.319, K.362, F.375, D.378, F.379, R.382 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:E.319, B:K.362, B:D.378, B:R.382 Water bridges: B:K.362 GOL.11: 7 residues within 4Å: Chain B: L.313, P.315, C.325, Q.326, K.327, W.328, S.329 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Water bridges: A:S.93, A:S.93 Hydrogen bonds: B:L.313, B:C.325 GOL.12: 2 residues within 4Å: Chain B: A.22, R.23 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.23

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Neeb, M. et al., Addressing a New Subpocket of TGT by Elongated 2-Amino-lin-benzoguanines. To be Published

Release Date

2015-05-20

Peptides

Queuine tRNA-ribosyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Queuine tRNA-ribosyltransferase

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