SMTL ID : 4hqv.1

tRNA-guanine transglycosylase Y106F, C158V, V233G mutant in complex with queuine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.66 Å

Oligo State

homo-dimer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.317, C.319, C.322, H.348 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.317, A:C.319, A:C.322, A:H.348 ZN.7: 4 residues within 4Å: Chain B: C.317, C.319, C.322, H.348 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.317, B:C.319, B:C.322, B:H.348

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 6 residues within 4Å: Chain A: P.55, E.56, G.93, W.94, D.95, R.96 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:P.55, A:G.93, A:D.95, A:R.96 Water bridges: A:E.56, A:R.96 GOL.3: 4 residues within 4Å: Chain A: A.218, M.249, L.250, P.251 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.214 GOL.4: 3 residues within 4Å: Chain A: P.251, D.253, K.254 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.253, A:K.254 Water bridges: A:Y.225 GOL.5: 7 residues within 4Å: Chain A: W.295, E.316, K.359, F.372, D.375, F.376, R.379 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.316, A:D.375, A:R.379 Water bridges: A:K.359 GOL.8: 6 residues within 4Å: Chain B: P.55, E.56, G.93, W.94, D.95, R.96 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:P.55, B:G.93, B:D.95, B:R.96 Water bridges: B:E.56, B:R.96 GOL.9: 4 residues within 4Å: Chain B: A.218, M.249, L.250, P.251 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:A.214 GOL.10: 3 residues within 4Å: Chain B: P.251, D.253, K.254 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.253, B:K.254 GOL.11: 7 residues within 4Å: Chain B: W.295, E.316, K.359, F.372, D.375, F.376, R.379 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.316, B:D.375, B:R.379 Water bridges: B:K.359

2 x QEI: 2-amino-5-({[(1S,4S,5R)-4,5-dihydroxycyclopent-2-en-1-yl]amino}methyl)-3,7-dihydro-4H-pyrrolo[2,3-d]pyrimidin-4-one(Non-covalent)

QEI.6: 10 residues within 4Å: Chain A: S.102, F.105, D.155, V.157, I.200, Q.202, G.228, G.229, L.230, M.259 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:M.259 Hydrogen bonds: A:S.102, A:Q.202, A:G.229, A:L.230 Water bridges: A:S.102, A:S.102, A:G.103, A:M.259 Salt bridges: A:D.155 pi-Stacking: A:F.105 QEI.12: 10 residues within 4Å: Chain B: S.102, F.105, D.155, V.157, I.200, Q.202, G.228, G.229, L.230, M.259 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:M.259 Hydrogen bonds: B:S.102, B:Q.202, B:G.229, B:L.230 Water bridges: B:S.102, B:S.102, B:G.103, B:M.259 Salt bridges: B:D.155 pi-Stacking: B:F.105

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Biela, I. et al., Investigation of Specificity Determinants in Bacterial tRNA-Guanine Transglycosylase Reveals Queuine, the Substrate of Its Eucaryotic Counterpart, as Inhibitor. Plos One (2013)

Release Date

2012-11-21

Peptides

Queuine tRNA-ribosyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Queuine tRNA-ribosyltransferase