SMTL ID : 4q8u.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.31 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.10: 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

14 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 7 residues within 4Å: Chain A: P.56, E.57, G.94, W.95, D.96, R.97 Chain B: K.325 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:G.94, A:D.96, A:R.97 Water bridges: A:E.57, A:E.57, B:K.325, B:K.325 GOL.3: 4 residues within 4Å: Chain A: F.16, S.17, I.18, D.254 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:I.18, A:I.18, A:D.254 Water bridges: A:R.21, A:R.21 GOL.4: 6 residues within 4Å: Chain A: A.61, T.62, C.320, A.321, E.348, A.352 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:A.321, A:E.348, A:E.348 Water bridges: A:A.61, A:T.62, A:T.62, A:H.319, A:Q.356 GOL.5: 6 residues within 4Å: Chain A: L.311, P.313, C.323, Q.324, W.326, S.327 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:C.323 Water bridges: A:S.327 GOL.6: 6 residues within 4Å: Chain A: R.11, M.32, K.33, R.34, G.35, V.36 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.11, A:R.11, A:M.32 Water bridges: A:V.36 GOL.7: 7 residues within 4Å: Chain A: W.296, E.317, K.360, F.373, D.376, F.377, R.380 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.317, A:D.376 Water bridges: A:E.317 GOL.8: 3 residues within 4Å: Chain A: R.38, R.60, G.63 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.38, A:R.38, A:R.60 Water bridges: A:R.60, A:Q.359 GOL.11: 7 residues within 4Å: Chain A: K.325 Chain B: P.56, E.57, G.94, W.95, D.96, R.97 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:G.94, B:D.96, B:R.97 Water bridges: B:E.57, A:K.325, A:K.325, A:K.325 GOL.12: 4 residues within 4Å: Chain B: F.16, S.17, I.18, D.254 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:I.18, B:I.18, B:D.254 Water bridges: B:R.21, B:R.21 GOL.13: 6 residues within 4Å: Chain B: A.61, T.62, C.320, A.321, E.348, A.352 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:A.321, B:E.348 Water bridges: B:A.61, B:T.62, B:T.62, B:H.319, B:Q.356 GOL.14: 6 residues within 4Å: Chain B: L.311, P.313, C.323, Q.324, W.326, S.327 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:C.323 Water bridges: B:S.327 GOL.15: 6 residues within 4Å: Chain B: R.11, M.32, K.33, R.34, G.35, V.36 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.11, B:M.32 Water bridges: B:V.36 GOL.16: 7 residues within 4Å: Chain B: W.296, E.317, K.360, F.373, D.376, F.377, R.380 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.317, B:D.376 Water bridges: B:K.360 GOL.17: 3 residues within 4Å: Chain B: R.38, R.60, G.63 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.38, B:R.38, B:R.60 Water bridges: B:R.60, B:Q.359

2 x 2YW: methyl 4-{2-[(6-amino-8-oxo-7,8-dihydro-1H-imidazo[4,5-g]quinazolin-2-yl)amino]ethyl}benzoate(Non-covalent)

2YW.9: 15 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, G.234, M.260, G.261 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:S.103, A:Q.203, A:G.230, A:L.231, A:A.232 Salt bridges: A:D.102, A:D.156 pi-Stacking: A:Y.106, A:Y.106 2YW.18: 15 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, G.234, M.260, G.261 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:S.103, B:Q.203, B:G.230, B:L.231, B:A.232 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

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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