SMTL ID : 1pxg.1

Crystal structure of the mutated tRNA-guanine transglycosylase (TGT) D280E complexed with preQ1

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.317, C.319, C.322, H.348 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.317, A:C.319, A:C.322, A:H.348 ZN.11: 4 residues within 4Å: Chain B: C.317, C.319, C.322, H.348 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.317, B:C.319, B:C.322, B:H.348

2 x PRF: 7-DEAZA-7-AMINOMETHYL-GUANINE(Non-covalent)

PRF.2: 10 residues within 4Å: Chain A: Y.105, D.155, C.157, Q.202, G.228, G.229, L.230, V.232, M.259, G.260 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:M.259 Hydrogen bonds: A:Y.105, A:Q.202, A:G.229, A:L.230 Water bridges: A:S.102, A:S.102, A:S.102, A:D.155, A:D.155, A:L.230 Salt bridges: A:D.155 PRF.12: 10 residues within 4Å: Chain B: Y.105, D.155, C.157, Q.202, G.228, G.229, L.230, V.232, M.259, G.260 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:M.259 Hydrogen bonds: B:Y.105, B:Q.202, B:G.229, B:L.230 Water bridges: B:S.102, B:S.102, B:S.102, B:D.155, B:D.155, B:L.230 Salt bridges: B:D.155

16 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain A: P.55, E.56, G.93, W.94, D.95, R.96 Ligand excluded by PLIP GOL.4: 6 residues within 4Å: Chain A: R.10, M.31, K.32, R.33, G.34, V.35 Ligand excluded by PLIP GOL.5: 4 residues within 4Å: Chain A: F.15, S.16, I.17, D.253 Ligand excluded by PLIP GOL.6: 4 residues within 4Å: Chain A: H.332, R.335, A.336 Chain B: P.77 Ligand excluded by PLIP GOL.7: 6 residues within 4Å: Chain A: W.295, E.316, K.359, F.372, F.376, R.379 Ligand excluded by PLIP GOL.8: 3 residues within 4Å: Chain A: P.251, D.253, K.254 Ligand excluded by PLIP GOL.9: 6 residues within 4Å: Chain A: A.60, T.61, C.319, A.320, E.347, A.351 Ligand excluded by PLIP GOL.10: 3 residues within 4Å: Chain A: R.37, R.59, G.62 Ligand excluded by PLIP GOL.13: 6 residues within 4Å: Chain B: P.55, E.56, G.93, W.94, D.95, R.96 Ligand excluded by PLIP GOL.14: 6 residues within 4Å: Chain B: R.10, M.31, K.32, R.33, G.34, V.35 Ligand excluded by PLIP GOL.15: 4 residues within 4Å: Chain B: F.15, S.16, I.17, D.253 Ligand excluded by PLIP GOL.16: 4 residues within 4Å: Chain A: P.77 Chain B: H.332, R.335, A.336 Ligand excluded by PLIP GOL.17: 6 residues within 4Å: Chain B: W.295, E.316, K.359, F.372, F.376, R.379 Ligand excluded by PLIP GOL.18: 3 residues within 4Å: Chain B: P.251, D.253, K.254 Ligand excluded by PLIP GOL.19: 6 residues within 4Å: Chain B: A.60, T.61, C.319, A.320, E.347, A.351 Ligand excluded by PLIP GOL.20: 3 residues within 4Å: Chain B: R.37, R.59, G.62 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kittendorf, J.D. et al., An essential role for aspartate 264 in catalysis by tRNA-guanine transglycosylase from Escherichia coli. J.Biol.Chem. (2003)

Release Date

2003-09-09

Peptides

Queuine tRNA-ribosyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Queuine tRNA-ribosyltransferase