SMTL ID : 4l56.1

tRNA guanine transglycosylase H333D mutant apo structure

Coordinates

PDB Format Compare

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.320, C.322, C.325, H.351 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.320, A:C.322, A:C.325, A:H.351 ZN.9: 4 residues within 4Å: Chain B: C.320, C.322, C.325, H.351 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.320, B:C.322, B:C.325, B:H.351

14 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 7 residues within 4Å: Chain A: P.58, E.59, R.62, G.96, W.97, D.98, R.99 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.98, A:D.98, A:R.99 GOL.3: 7 residues within 4Å: Chain A: G.107, Q.119, V.124, D.158, E.159, C.160, W.180 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.119, A:C.160 GOL.4: 7 residues within 4Å: Chain A: W.298, E.319, K.362, F.375, D.378, F.379, R.382 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.319, A:D.378 Water bridges: A:K.362 GOL.5: 4 residues within 4Å: Chain A: Q.119, S.120, E.121, R.176 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.121, A:R.176, A:R.176 GOL.6: 5 residues within 4Å: Chain A: R.36, H.147, G.150, S.151, Q.194 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.36, A:R.36, A:H.147 Water bridges: A:Q.194 GOL.7: 6 residues within 4Å: Chain A: R.40, T.64, G.65, Q.357, Q.358, Q.361 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.40, A:R.40, A:Q.357 Water bridges: A:Q.358 GOL.8: 2 residues within 4Å: Chain A: K.192, E.196 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.192, A:K.192 GOL.10: 7 residues within 4Å: Chain B: P.58, E.59, R.62, G.96, W.97, D.98, R.99 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.98, B:D.98, B:R.99 GOL.11: 7 residues within 4Å: Chain B: G.107, Q.119, V.124, D.158, E.159, C.160, W.180 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.119, B:C.160 GOL.12: 7 residues within 4Å: Chain B: W.298, E.319, K.362, F.375, D.378, F.379, R.382 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.319, B:D.378 Water bridges: B:K.362 GOL.13: 4 residues within 4Å: Chain B: Q.119, S.120, E.121, R.176 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.121, B:R.176, B:R.176 GOL.14: 5 residues within 4Å: Chain B: R.36, H.147, G.150, S.151, Q.194 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.36, B:R.36, B:H.147, B:H.147 Water bridges: B:Q.194 GOL.15: 6 residues within 4Å: Chain B: R.40, T.64, G.65, Q.357, Q.358, Q.361 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.40, B:R.40, B:Q.357 Water bridges: B:Q.358 GOL.16: 2 residues within 4Å: Chain B: K.192, E.196 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.192, B:K.192

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jakobi, S. et al., What Glues a Homodimer Together: Systematic Analysis of the Stabilizing Effect of an Aromatic Hot Spot in the Protein-Protein Interface of the tRNA-Modifying Enzyme Tgt. Acs Chem.Biol. (2015)

Release Date

2014-12-24

Peptides

Queuine tRNA-ribosyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Queuine tRNA-ribosyltransferase