SMTL ID : 4e2v.1

tRNA-guanine transglycosylase Y106F, C158V mutant in complex with preQ1

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.18 Å

Oligo State

homo-dimer

Ligands

2 x PRF: 7-DEAZA-7-AMINOMETHYL-GUANINE(Non-covalent)

PRF.1: 11 residues within 4Å: Chain A: S.103, G.105, F.106, D.156, V.158, I.201, Q.203, G.229, G.230, L.231, M.260 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:F.106, A:M.260 Hydrogen bonds: A:S.103, A:G.105, A:F.106, A:Q.203, A:G.230, A:L.231 Water bridges: A:S.103, A:S.103, A:S.103, A:G.104, A:Q.107, A:M.260, A:G.261, A:D.280 Salt bridges: A:D.156 pi-Stacking: A:F.106 PRF.7: 11 residues within 4Å: Chain B: S.103, G.105, F.106, D.156, V.158, I.201, Q.203, G.229, G.230, L.231, M.260 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:F.106, B:M.260 Hydrogen bonds: B:S.103, B:G.105, B:F.106, B:Q.203, B:G.230, B:L.231 Water bridges: B:S.103, B:S.103, B:S.103, B:G.104, B:Q.107, B:M.260, B:G.261, B:D.280 Salt bridges: B:D.156 pi-Stacking: B:F.106

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 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:D.96, 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 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.254, A:K.255 GOL.4: 7 residues within 4Å: Chain A: W.296, E.317, K.360, F.373, D.376, F.377, R.380 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.317, A:K.360, A:D.376, A:R.380 Water bridges: A:E.317 GOL.6: 5 residues within 4Å: Chain A: A.305, S.308, H.332, R.336 Chain B: R.82 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:R.82, B:R.82, A:H.332 Water bridges: A:S.308 GOL.8: 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:D.96, B:D.96, B:R.97 Water bridges: B:E.57, B:R.97 GOL.9: 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.10: 7 residues within 4Å: Chain B: W.296, E.317, K.360, F.373, D.376, F.377, R.380 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:E.317, B:K.360, B:D.376, B:R.380 Water bridges: B:K.360 GOL.12: 5 residues within 4Å: Chain A: R.82 Chain B: A.305, S.308, H.332, R.336 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.82, A:R.82, B:H.332 Water bridges: B:S.308

2 x ZN: ZINC ION(Non-covalent)

ZN.5: 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.11: 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

2013-03-27

Peptides

Queuine tRNA-ribosyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Queuine tRNA-ribosyltransferase

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