SMTL ID : 2z1w.1

tRNA guanine transglycosylase TGT E235Q mutant in complex with BDI (2-BUTYL-5,6-DIHYDRO-1H-IMIDAZO[4,5-D]PYRIDAZINE-4,7-DIONE)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.63 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.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 BDI: 2-BUTYL-5,6-DIHYDRO-1H-IMIDAZO[4,5-D]PYRIDAZINE-4,7-DIONE(Non-covalent)

BDI.2: 12 residues within 4Å: Chain A: D.102, Y.106, D.156, C.158, I.201, Q.203, G.229, G.230, A.232, M.260, G.261 Ligands: GOL.4 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:Y.106, A:Y.106 Hydrogen bonds: A:Q.203, A:G.230 Water bridges: A:S.103, A:G.105, A:L.231, A:M.260 pi-Stacking: A:Y.106 BDI.13: 12 residues within 4Å: Chain B: D.102, Y.106, D.156, C.158, I.201, Q.203, G.229, G.230, A.232, M.260, G.261 Ligands: GOL.15 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:Y.106, B:Y.106 Hydrogen bonds: B:Q.203, B:G.230 Water bridges: B:S.103, B:G.105, B:L.231, B:M.260 pi-Stacking: B:Y.106

18 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 Ligand excluded by PLIP GOL.4: 10 residues within 4Å: Chain A: V.45, L.68, D.102, Q.107, Y.258, M.260, G.261, D.280, C.281 Ligands: BDI.2 Ligand excluded by PLIP GOL.5: 9 residues within 4Å: Chain A: H.145, G.148, S.149, D.150, E.191, Q.192, N.195, A.196 Ligands: GOL.7 Ligand excluded by PLIP GOL.6: 6 residues within 4Å: Chain A: E.317, K.360, F.373, D.376, F.377, R.380 Ligand excluded by PLIP GOL.7: 6 residues within 4Å: Chain A: R.34, G.87, G.88, L.147, G.148 Ligands: GOL.5 Ligand excluded by PLIP GOL.8: 6 residues within 4Å: Chain A: A.61, T.62, H.319, C.320, A.352, Q.356 Ligand excluded by PLIP GOL.9: 5 residues within 4Å: Chain A: M.176, K.180, A.217, E.220, I.221 Ligand excluded by PLIP GOL.10: 2 residues within 4Å: Chain A: K.24, E.273 Ligand excluded by PLIP GOL.11: 5 residues within 4Å: Chain A: P.249, M.250, L.251, P.252, D.253 Ligand excluded by PLIP GOL.14: 6 residues within 4Å: Chain B: P.56, E.57, G.94, W.95, D.96, R.97 Ligand excluded by PLIP GOL.15: 10 residues within 4Å: Chain B: V.45, L.68, D.102, Q.107, Y.258, M.260, G.261, D.280, C.281 Ligands: BDI.13 Ligand excluded by PLIP GOL.16: 9 residues within 4Å: Chain B: H.145, G.148, S.149, D.150, E.191, Q.192, N.195, A.196 Ligands: GOL.18 Ligand excluded by PLIP GOL.17: 6 residues within 4Å: Chain B: E.317, K.360, F.373, D.376, F.377, R.380 Ligand excluded by PLIP GOL.18: 6 residues within 4Å: Chain B: R.34, G.87, G.88, L.147, G.148 Ligands: GOL.16 Ligand excluded by PLIP GOL.19: 6 residues within 4Å: Chain B: A.61, T.62, H.319, C.320, A.352, Q.356 Ligand excluded by PLIP GOL.20: 5 residues within 4Å: Chain B: M.176, K.180, A.217, E.220, I.221 Ligand excluded by PLIP GOL.21: 2 residues within 4Å: Chain B: K.24, E.273 Ligand excluded by PLIP GOL.22: 5 residues within 4Å: Chain B: P.249, M.250, L.251, P.252, D.253 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tidten, N. et al., Glutamate versus Glutamine Exchange Swaps Substrate Selectivity in tRNA-Guanine Transglycosylase: Insight into the Regulation of Substrate Selectivity by Kinetic and Crystallographic Studies. J.Mol.Biol. (2007)

Release Date

2007-11-06

Peptides

Queuine tRNA-ribosyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Queuine tRNA-ribosyltransferase

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