SMTL ID : 5egr.1

tRNA guanine transglycosylase (TGT) in complex with an Immucillin derivative

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

homo-dimer

Ligands

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 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: 2 interactions with chain B, 4 interactions with chain A Water bridges: B:K.325, B:K.325, A:R.97 Hydrogen bonds: A:D.96, A:D.96, A:R.97 GOL.2: 6 residues within 4Å: Chain A: W.296, E.317, K.360, F.373, 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.3: 7 residues within 4Å: Chain A: L.311, P.313, C.323, Q.324, K.325, W.326, S.327 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:C.323 GOL.4: 5 residues within 4Å: Chain A: A.61, H.319, C.320, A.321, E.348 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.61, A:A.321, A:E.348, A:E.348 GOL.8: 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: 4 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:D.96, B:D.96, B:R.97 Water bridges: B:R.97, A:K.325, A:K.325 GOL.9: 6 residues within 4Å: Chain B: W.296, E.317, K.360, F.373, 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.10: 7 residues within 4Å: Chain B: L.311, P.313, C.323, Q.324, K.325, W.326, S.327 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:C.323 GOL.11: 5 residues within 4Å: Chain B: A.61, H.319, C.320, A.321, E.348 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:A.61, B:A.321, B:E.348

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.12: 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

2 x 5NT: 2-azanyl-7-[(2~{S},3~{R},5~{S})-5-(hydroxymethyl)-3-oxidanyl-pyrrolidin-2-yl]-3,5-dihydropyrrolo[3,2-d]pyrimidin-4-one(Non-covalent)

5NT.6: 12 residues within 4Å: Chain A: N.70, D.102, S.103, Y.106, D.156, I.201, Q.203, G.229, G.230, M.260, G.261, D.280 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:D.102, A:S.103, A:Y.106, A:Q.203, A:G.230, A:G.261, A:D.280 Water bridges: A:G.104, A:Q.107, A:D.156 Salt bridges: A:D.102, A:D.156 pi-Stacking: A:Y.106, A:Y.106 5NT.13: 12 residues within 4Å: Chain B: N.70, D.102, S.103, Y.106, D.156, I.201, Q.203, G.229, G.230, M.260, G.261, D.280 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:D.102, B:D.102, B:S.103, B:Y.106, B:Q.203, B:G.230, B:G.261, B:D.280 Water bridges: B:G.104, B:Q.107, B:D.156 Salt bridges: B:D.102, B:D.156 pi-Stacking: B:Y.106, B:Y.106

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.7: 5 residues within 4Å: Chain A: P.249, M.250, L.251, P.252, D.253 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:M.250, A:D.253 EDO.14: 5 residues within 4Å: Chain B: P.249, M.250, L.251, P.252, D.253 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:M.250, B:D.253

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ehrmann, F.R. et al., Synthesis of an Immucillin Derivative as a Class of tRNA-Guanine Transglycosylase Inhibitors: Exploration of a Transition State Analogous Binding Mode. To be Published

Release Date

2016-11-09

Peptides

Queuine tRNA-ribosyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Queuine tRNA-ribosyltransferase

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