SMTL ID : 5i02.1

tRNA guanine transglycosylase (TGT) in co-crystallized complex with 6-amino-4-{2-[(cyclohexylmethyl)amino]ethyl}-2-(methylamino)-1,7-dihydro-8H-imidazo[4,5-g]quinazolin-8-one

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.25 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.9: 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 PK2: 6-amino-4-{2-[(cyclohexylmethyl)amino]ethyl}-2-(methylamino)-1,7-dihydro-8H-imidazo[4,5-g]quinazolin-8-one(Non-covalent)

PK2.2: 19 residues within 4Å: Chain A: L.68, G.69, N.70, D.102, S.103, Y.106, Q.107, D.156, C.158, I.201, Q.203, G.229, G.230, L.231, A.232, M.260, G.261, D.280, V.282 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:L.68, A:Y.106, A:V.282 Hydrogen bonds: A:S.103, A:Q.203, A:G.230, A:L.231, A:A.232, A:D.280 Water bridges: A:D.156, A:L.231 Salt bridges: A:D.102, A:D.156 pi-Stacking: A:Y.106, A:Y.106 PK2.10: 19 residues within 4Å: Chain B: L.68, G.69, N.70, D.102, S.103, Y.106, Q.107, D.156, C.158, I.201, Q.203, G.229, G.230, L.231, A.232, M.260, G.261, D.280, V.282 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:L.68, B:Y.106, B:V.282 Hydrogen bonds: B:S.103, B:Q.203, B:G.230, B:L.231, B:A.232, B:D.280 Water bridges: B:D.156, B:L.231 Salt bridges: B:D.102, B:D.156 pi-Stacking: B:Y.106, B:Y.106

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

EDO.3: 7 residues within 4Å: Chain A: T.27, G.28, T.29, R.38, T.39, R.362 Ligands: EDO.4 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.27, A:G.28, A:T.39 Water bridges: A:S.366 EDO.4: 5 residues within 4Å: Chain A: Q.359, R.362, D.363, S.366 Ligands: EDO.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.359, A:R.362, A:D.363 EDO.5: 3 residues within 4Å: Chain A: H.145, L.146, E.191 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.191 Water bridges: A:E.191 EDO.11: 7 residues within 4Å: Chain B: T.27, G.28, T.29, R.38, T.39, R.362 Ligands: EDO.12 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.28, B:T.39 Water bridges: B:S.366 EDO.12: 5 residues within 4Å: Chain B: Q.359, R.362, D.363, S.366 Ligands: EDO.11 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.359, B:R.362 EDO.13: 3 residues within 4Å: Chain B: H.145, L.146, E.191 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.191

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 4 residues within 4Å: Chain A: Q.117, S.118, E.119, R.174 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.119, A:R.174, A:R.174 GOL.7: 7 residues within 4Å: Chain A: H.145, G.148, S.149, E.191, Q.192, N.195, A.196 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.145, A:E.191, A:Q.192 GOL.14: 4 residues within 4Å: Chain B: Q.117, S.118, E.119, R.174 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.119, B:R.174, B:R.174 GOL.15: 7 residues within 4Å: Chain B: H.145, G.148, S.149, E.191, Q.192, N.195, A.196 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:H.145, B:H.145, B:E.191, B:Q.192

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

CL.8: 5 residues within 4Å: Chain A: T.71, Y.72, D.102, G.104, Q.107 Ligand excluded by PLIP CL.16: 5 residues within 4Å: Chain B: T.71, Y.72, D.102, G.104, Q.107 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ehrmann, F.R. et al., Co-crystallization, Isothermal titration calorimetry and nanoESI-MS reveal dimer disturbing inhibitors. To be Published

Release Date

2017-02-15

Peptides

Queuine tRNA-ribosyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Queuine tRNA-ribosyltransferase

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