SMTL ID : 3gc4.1

tRNA-guanine transglycosylase in complex with inhibitor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

2 x AAQ: 6-amino-4-[2-(benzylamino)ethyl]-2-(methylamino)-1,7-dihydro-8H-imidazo[4,5-g]quinazolin-8-one(Non-covalent)

AAQ.1: 20 residues within 4Å: Chain A: V.45, T.47, L.68, N.70, H.73, 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, D.280 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:V.45, A:Y.106, A:Y.106, A:Y.106, A:M.260 Hydrogen bonds: A:S.103, A:Y.106, A:Q.203, A:G.230, A:L.231, A:A.232, A:D.280 Water bridges: A:G.104, A:L.231 Salt bridges: A:D.102, A:D.156 pi-Stacking: A:Y.106, A:Y.106 AAQ.8: 20 residues within 4Å: Chain B: V.45, T.47, L.68, N.70, H.73, 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, D.280 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:V.45, B:Y.106, B:Y.106, B:Y.106, B:M.260 Hydrogen bonds: B:S.103, B:Y.106, B:Y.106, B:Q.203, B:G.230, B:L.231, B:A.232, B:D.280 Water bridges: B:G.104, B:L.231 Salt bridges: B:D.102, B:D.156 pi-Stacking: B:Y.106, B:Y.106

2 x ZN: ZINC ION(Non-covalent)

ZN.2: 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.9: 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

10 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 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: 5 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:G.94, B:D.96, B:R.97, A:K.325 Water bridges: B:E.57, B:R.97, A:K.325 GOL.4: 8 residues within 4Å: Chain A: A.19, T.27, G.28, T.29, R.38, T.39, R.362, S.366 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.27, A:G.28, A:T.39, A:S.366 Water bridges: A:S.366 GOL.5: 3 residues within 4Å: Chain A: E.119, R.174, R.177 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.174 GOL.6: 5 residues within 4Å: Chain A: F.241, G.270, E.273, R.274, R.378 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.273, A:R.274, A:R.274 GOL.7: 4 residues within 4Å: Chain A: Q.117, S.118, E.119, R.174 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.119, A:R.174, A:R.174 GOL.10: 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, B:K.325 Water bridges: A:E.57, A:R.97, B:K.325 GOL.11: 8 residues within 4Å: Chain B: A.19, T.27, G.28, T.29, R.38, T.39, R.362, S.366 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.28, B:T.39, B:S.366 Water bridges: B:S.366 GOL.12: 3 residues within 4Å: Chain B: E.119, R.174, R.177 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.119, B:R.174 GOL.13: 5 residues within 4Å: Chain B: F.241, G.270, E.273, R.274, R.378 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.273, B:R.274, B:R.274 GOL.14: 4 residues within 4Å: Chain B: Q.117, S.118, E.119, R.174 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.119, B:R.174, B:R.174

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ritschel, T. et al., How to Replace the Residual Solvation Shell of Polar Active Site Residues to Achieve Nanomolar Inhibition of tRNA-Guanine Transglycosylase. Chemmedchem (2009)

Release Date

2009-12-15

Peptides

Queuine tRNA-ribosyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Queuine tRNA-ribosyltransferase

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