SMTL ID : 5jxq.1

TRNA-GUANINE TRANSGLYCOSYLASE (TGT) IN COMPLEX WITH 6-AMINO-2-{[4-(2-HYDROXYETHYL)PHENETHYL]AMINO}-1,7-DIHYDRO-8H-IMIDAZO[4,5-g]QUINAZOLIN-8-ONE

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.20 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.7: 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: 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.3: 7 residues within 4Å: Chain A: K.325 Chain B: P.56, E.57, 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:D.96, B:D.96, B:R.97, A:K.325 Water bridges: B:E.57 GOL.4: 7 residues within 4Å: Chain A: L.311, P.313, C.323, Q.324, K.325, W.326, S.327 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:C.323 Water bridges: B:S.91, B:S.91 GOL.8: 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.9: 7 residues within 4Å: Chain A: P.56, E.57, G.94, W.95, D.96, R.97 Chain B: K.325 6 PLIP interactions: 1 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:K.325, A:P.56, A:D.96, A:D.96, A:R.97 Water bridges: A:E.57 GOL.10: 7 residues within 4Å: Chain B: L.311, P.313, C.323, Q.324, K.325, W.326, S.327 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Water bridges: A:S.91, A:S.91 Hydrogen bonds: B:C.323

2 x 6OK: 6-amino-2-({2-[4-(2-hydroxyethyl)phenyl]ethyl}amino)-1,7-dihydro-8H-imidazo[4,5-g]quinazolin-8-one(Non-covalent)

6OK.5: 17 residues within 4Å: Chain A: D.102, S.103, Y.106, D.156, C.158, I.201, Q.203, G.229, G.230, L.231, A.232, M.260, G.261, C.281, V.282, L.283, R.286 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:V.282 Hydrogen bonds: A:S.103, A:Q.203, A:G.230, A:L.231, A:A.232 Water bridges: A:L.231 Salt bridges: A:D.102, A:D.156 pi-Stacking: A:Y.106, A:Y.106 6OK.11: 17 residues within 4Å: Chain B: D.102, S.103, Y.106, D.156, C.158, I.201, Q.203, G.229, G.230, L.231, A.232, M.260, G.261, C.281, V.282, L.283, R.286 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:V.282 Hydrogen bonds: B:S.103, B:Q.203, B:G.230, B:L.231, B:A.232 Water bridges: B:D.102, B:Y.106, B:L.231 Salt bridges: B:D.102, B:D.156 pi-Stacking: B:Y.106, B:Y.106

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.6: 5 residues within 4Å: Chain A: K.52, V.282, T.285, R.286, R.289 Ligand excluded by PLIP CL.12: 5 residues within 4Å: Chain B: K.52, V.282, T.285, R.286, R.289 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Neeb, M. et al., Occupying a flat subpocket in a tRNA-modifying enzyme with ordered or disordered side chains: Favorable or unfavorable for binding?. Bioorg.Med.Chem. (2016)

Release Date

2016-08-10

Peptides

Queuine tRNA-ribosyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Queuine tRNA-ribosyltransferase

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