SMTL ID : 4pum.1

tRNA-Guanine Transglycosylase (TGT) Mutant D156N in Complex with 6-Amino-2-(methylamino)-1H,7H,8H-imidazo[4,5-g]quinazolin-8-one

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.93 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.5: 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

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 7 residues within 4Å: Chain A: P.58, E.59, G.96, W.97, D.98, R.99 Chain B: K.327 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:G.96, A:D.98, A:R.99, B:K.327 Water bridges: A:E.59, A:E.59, A:R.99 GOL.3: 6 residues within 4Å: Chain A: 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.6: 7 residues within 4Å: Chain A: K.327 Chain B: P.58, E.59, G.96, W.97, D.98, R.99 7 PLIP interactions: 1 interactions with chain A, 6 interactions with chain B Hydrogen bonds: A:K.327, B:G.96, B:D.98, B:R.99 Water bridges: B:E.59, B:E.59, B:R.99 GOL.7: 6 residues within 4Å: Chain B: 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

2 x 2WU: 6-amino-2-(methylamino)-3,7-dihydro-8H-imidazo[4,5-g]quinazolin-8-one(Non-covalent)

2WU.4: 13 residues within 4Å: Chain A: D.104, S.105, Y.108, N.158, C.160, I.203, Q.205, G.231, G.232, L.233, A.234, M.262, G.263 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:Y.108, A:M.262 Hydrogen bonds: A:Y.108, A:N.158, A:N.158, A:N.158, A:Q.205, A:G.232, A:A.234 Water bridges: A:L.233 Salt bridges: A:D.104 pi-Stacking: A:Y.108, A:Y.108 2WU.8: 13 residues within 4Å: Chain B: D.104, S.105, Y.108, N.158, C.160, I.203, Q.205, G.231, G.232, L.233, A.234, M.262, G.263 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:Y.108, B:M.262 Hydrogen bonds: B:Y.108, B:N.158, B:N.158, B:N.158, B:Q.205, B:G.232, B:A.234 Water bridges: B:L.233 Salt bridges: B:D.104 pi-Stacking: B:Y.108, B:Y.108

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Neeb, M. et al., Chasing Protons: How Isothermal Titration Calorimetry, Mutagenesis, and pKa Calculations Trace the Locus of Charge in Ligand Binding to a tRNA-Binding Enzyme. J.Med.Chem. (2014)

Release Date

2014-07-16

Peptides

Queuine tRNA-ribosyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Queuine tRNA-ribosyltransferase