SMTL ID : 5uti.1

Crystal Structure of TGT in complex with fragment in preQ1 pocket

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.36 Å

Oligo State

homo-dimer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: C.309, C.311, V.313, C.314, H.340 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.309, A:C.311, A:C.314, A:H.340 ZN.6: 5 residues within 4Å: Chain B: C.309, C.311, V.313, C.314, H.340 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.309, B:C.311, B:C.314, B:H.340

2 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.2: 4 residues within 4Å: Chain A: F.7, S.8, I.9, D.245 No protein-ligand interaction detected (PLIP) DMS.7: 4 residues within 4Å: Chain B: F.7, S.8, I.9, D.245 No protein-ligand interaction detected (PLIP)

2 x GGB: L-CANAVANINE(Non-covalent)

GGB.3: 15 residues within 4Å: Chain A: D.93, S.94, Y.97, D.147, C.149, I.192, Q.194, V.219, G.220, G.221, L.222, A.223, V.224, M.251, G.252 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:M.251 Hydrogen bonds: A:S.94, A:G.221, A:L.222, A:M.251 Water bridges: A:G.95 Salt bridges: A:D.93, A:D.147 GGB.8: 15 residues within 4Å: Chain B: D.93, S.94, Y.97, D.147, C.149, I.192, Q.194, V.219, G.220, G.221, L.222, A.223, V.224, M.251, G.252 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:M.251 Hydrogen bonds: B:S.94, B:G.221, B:L.222, B:M.251 Water bridges: B:G.95 Salt bridges: B:D.93, B:D.147

2 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.4: 7 residues within 4Å: Chain A: L.302, P.304, C.314, Q.315, K.316, W.317, S.318 No protein-ligand interaction detected (PLIP) PGE.9: 7 residues within 4Å: Chain B: L.302, P.304, C.314, Q.315, K.316, W.317, S.318 No protein-ligand interaction detected (PLIP)

2 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.5: 9 residues within 4Å: Chain A: W.287, E.308, H.310, Q.347, Q.350, K.351, F.364, F.368, R.371 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:W.287, A:K.351 Water bridges: A:H.310, A:R.371 PG4.10: 9 residues within 4Å: Chain B: W.287, E.308, H.310, Q.347, Q.350, K.351, F.364, F.368, R.371 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:W.287, B:K.351 Water bridges: B:H.310, B:R.371

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hassaan, E. et al., Fragments as Novel Starting Points for tRNA-Guanine Transglycosylase Inhibitors Found by Alternative Screening Strategies. Chemmedchem (2020)

Release Date

2018-03-07

Peptides

Queuine tRNA-ribosyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Queuine tRNA-ribosyltransferase

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