SMTL ID : 3rr4.1

tRNA-Guanine Transglycosylase in complex with N-Methyl-lin-Benzoguanine Inhibitor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.68 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.5: 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 HRD: 2,6-bis(methylamino)-1,7-dihydro-8H-imidazo[4,5-g]quinazolin-8-one(Non-covalent)

HRD.2: 13 residues within 4Å: Chain A: S.103, Y.106, D.156, C.158, I.201, Q.203, G.229, G.230, L.231, A.232, V.233, M.260, G.261 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:Y.106 Hydrogen bonds: A:D.156, A:D.156, A:Q.203, A:G.230, A:L.231, A:A.232 Water bridges: A:S.103, A:G.105, A:C.158, A:L.231 pi-Stacking: A:Y.106 HRD.6: 13 residues within 4Å: Chain B: S.103, Y.106, D.156, C.158, I.201, Q.203, G.229, G.230, L.231, A.232, V.233, M.260, G.261 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:Y.106 Hydrogen bonds: B:Y.106, B:D.156, B:D.156, B:Q.203, B:G.230, B:L.231, B:A.232 Water bridges: B:S.103, B:G.105, B:C.158, B:L.231 pi-Stacking: B:Y.106

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain A: P.56, E.57, G.94, W.95, D.96, R.97 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.96, A:D.96, A:R.97 Water bridges: A:E.57 GOL.4: 7 residues within 4Å: Chain A: A.337, E.339 Chain B: T.47, A.48, K.52, H.73, R.77 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:K.52, B:R.77, B:R.77, A:A.337 Water bridges: B:H.73 GOL.7: 6 residues within 4Å: Chain B: P.56, E.57, G.94, W.95, D.96, R.97 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.96, B:D.96, B:R.97 Water bridges: B:E.57 GOL.8: 7 residues within 4Å: Chain A: T.47, A.48, K.52, H.73, R.77 Chain B: A.337, E.339 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:A.337, B:E.339, A:K.52, A:R.77, A:R.77

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Barandun, L.J. et al., From lin-Benzoguanines to lin-Benzohypoxanthines as Ligands for Zymomonas mobilis tRNA-Guanine Transglycosylase: Replacement of Protein-Ligand Hydrogen Bonding by Importing Water Clusters. Chemistry (2012)

Release Date

2012-04-25

Peptides

Queuine tRNA-ribosyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Queuine tRNA-ribosyltransferase

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