SMTL ID : 3c2y.1

tRNA-Guanine Transglycosylase (TGT) in complex with 6-Amino-2-methyl-1,7-dihydro-imidazo[4,5-g]quinazolin-8-one

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.78 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.8: 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 S60: 6-amino-2-methyl-1,7-dihydro-8H-imidazo[4,5-g]quinazolin-8-one(Non-covalent)

S60.2: 13 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 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:Y.106, A:A.232, A:M.260 Hydrogen bonds: A:S.103, A:Q.203, A:G.230, A:L.231 Water bridges: A:G.104, A:Y.106, A:L.231 Salt bridges: A:D.102, A:D.156 S60.9: 13 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 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:Y.106, B:A.232, B:M.260 Hydrogen bonds: B:S.103, B:Q.203, B:G.230, B:L.231 Water bridges: B:D.102, B:G.104, B:Y.106, B:L.231 Salt bridges: B:D.102, B:D.156

10 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 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:P.56, A:D.96, A:D.96, A:R.97 Water bridges: A:E.57 GOL.4: 3 residues within 4Å: Chain A: P.252, D.254, K.255 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.255 Water bridges: A:Y.226, A:K.255 GOL.5: 7 residues within 4Å: Chain A: W.296, E.317, K.360, F.373, D.376, 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.6: 4 residues within 4Å: Chain A: E.173, M.176, R.177, A.217 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.173, A:R.177, A:R.177 GOL.7: 5 residues within 4Å: Chain A: F.241, G.270, E.273, R.274, R.378 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.273, A:R.274, A:R.274, A:R.378, A:R.378, A:R.378 GOL.10: 6 residues within 4Å: Chain B: P.56, E.57, G.94, W.95, D.96, R.97 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:P.56, B:D.96, B:D.96, B:R.97 Water bridges: B:E.57 GOL.11: 3 residues within 4Å: Chain B: P.252, D.254, K.255 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.255 Water bridges: B:K.255 GOL.12: 7 residues within 4Å: Chain B: W.296, E.317, K.360, F.373, D.376, 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.13: 4 residues within 4Å: Chain B: E.173, M.176, R.177, A.217 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.173, B:R.177, B:R.177 GOL.14: 5 residues within 4Å: Chain B: F.241, G.270, E.273, R.274, R.378 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:E.273, B:R.274, B:R.274, B:R.378, B:R.378, B:R.378

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ritschel, T. et al., Crystal structure analysis and in silico pKa calculations suggest strong pKa shifts of ligands as driving force for high-affinity binding to TGT. Chembiochem (2009)

Release Date

2009-02-03

Peptides

Queuine tRNA-ribosyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Queuine tRNA-ribosyltransferase

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