SMTL ID : 4h6e.1

tRNA-guanine transglycosylase Y106F, C158V, V233G mutant apo structure

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.42 Å

Oligo State

homo-dimer

Ligands

14 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 6 residues within 4Å: Chain A: P.56, E.57, G.94, W.95, D.96, R.97 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:P.56, A:G.94, A:D.96, A:R.97 Water bridges: A:E.57, A:R.97 GOL.3: 3 residues within 4Å: Chain A: P.252, D.254, K.255 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.254, A:K.255 Water bridges: A:Y.226 GOL.4: 7 residues within 4Å: Chain A: W.296, E.317, K.360, F.373, D.376, F.377, R.380 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.317, A:D.376, A:R.380 Water bridges: A:E.317 GOL.5: 5 residues within 4Å: Chain A: A.305, S.308, H.332, R.336 Chain B: R.82 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:R.82, B:R.82, A:H.332 Water bridges: A:S.308, A:R.336 GOL.6: 7 residues within 4Å: Chain A: R.34, G.148, S.149, D.150, E.191, N.195, A.196 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.34, A:R.34, A:D.150, A:D.150 Water bridges: A:H.145, A:H.145 GOL.7: 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.8: 5 residues within 4Å: Chain A: F.106, G.229, G.230, L.231, M.260 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.230, A:L.231 Water bridges: A:Q.203, A:Q.203, A:L.231 GOL.9: 6 residues within 4Å: Chain B: P.56, E.57, G.94, W.95, D.96, R.97 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:P.56, B:G.94, B:D.96, B:R.97 Water bridges: B:E.57, B:R.97 GOL.11: 3 residues within 4Å: Chain B: P.252, D.254, K.255 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.254, B:K.255 GOL.12: 7 residues within 4Å: Chain B: W.296, E.317, K.360, F.373, D.376, F.377, R.380 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.317, B:D.376, B:R.380 Water bridges: B:K.360 GOL.13: 5 residues within 4Å: Chain A: R.82 Chain B: A.305, S.308, H.332, R.336 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:H.332, A:R.82, A:R.82 Water bridges: B:S.308, B:R.336 GOL.14: 7 residues within 4Å: Chain B: R.34, G.148, S.149, D.150, E.191, N.195, A.196 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.34, B:R.34, B:D.150 Water bridges: B:H.145 GOL.15: 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.16: 5 residues within 4Å: Chain B: F.106, G.229, G.230, L.231, M.260 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:G.230, B:L.231 Water bridges: B:Q.203, B:Q.203, B:L.231

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.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

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

2012-11-07

Peptides

Queuine tRNA-ribosyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Queuine tRNA-ribosyltransferase

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