SMTL ID : 4hvx.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.82 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.6: 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

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 8 residues within 4Å: Chain A: P.56, E.57, R.60, G.94, W.95, D.96, R.97 Chain B: K.325 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:P.56, A:G.94, A:D.96, A:R.97, B:K.325 Water bridges: A:E.57 GOL.3: 7 residues within 4Å: Chain A: A.219, G.222, F.223, Y.226, P.252, D.254, K.255 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:A.219, A:Y.226, A:Y.226, A:D.254 Water bridges: A:K.255, A:K.255 GOL.4: 6 residues within 4Å: Chain A: H.145, G.148, S.149, E.191, Q.192, N.195 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.145 Water bridges: A:Q.192 GOL.7: 8 residues within 4Å: Chain A: K.325 Chain B: P.56, E.57, R.60, G.94, W.95, D.96, R.97 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:P.56, B:G.94, B:D.96, B:R.97, A:K.325 Water bridges: B:E.57 GOL.8: 7 residues within 4Å: Chain B: A.219, G.222, F.223, Y.226, P.252, D.254, K.255 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:A.219, B:Y.226, B:D.254 Water bridges: B:K.255, B:K.255 GOL.9: 6 residues within 4Å: Chain B: H.145, G.148, S.149, E.191, Q.192, N.195 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.145, B:H.145 Water bridges: B:Q.192

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.5: 10 residues within 4Å: Chain A: S.103, F.106, D.156, V.158, I.201, Q.203, G.229, G.230, L.231, M.260 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:M.260 Hydrogen bonds: A:S.103, A:G.105, A:Q.203, A:G.230, A:L.231 Water bridges: A:S.103, A:S.103, A:G.104, A:M.260 Salt bridges: A:D.156 pi-Stacking: A:F.106 QEI.10: 10 residues within 4Å: Chain B: S.103, F.106, D.156, V.158, I.201, Q.203, G.229, G.230, L.231, M.260 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:M.260 Hydrogen bonds: B:S.103, B:G.105, B:Q.203, B:G.230, B:L.231 Water bridges: B:S.103, B:S.103, B:G.104, B:M.260 Salt bridges: B:D.156 pi-Stacking: B:F.106

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

2012-12-26

Peptides

Queuine tRNA-ribosyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Queuine tRNA-ribosyltransferase

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