SMTL ID : 3uvi.1

tRNA-guanine transglycosylase C158S C281S W326E E339Q mutant

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.55 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.17: 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

16 x IOD: IODIDE ION(Non-functional Binders)

IOD.2: 2 residues within 4Å: Chain A: K.266, Y.383 Ligand excluded by PLIP IOD.3: 2 residues within 4Å: Chain A: A.55, L.56 Ligand excluded by PLIP IOD.4: 3 residues within 4Å: Chain A: A.234, G.236, G.238 Ligand excluded by PLIP IOD.5: 2 residues within 4Å: Chain A: V.250, P.251 Ligand excluded by PLIP IOD.6: 1 residues within 4Å: Chain A: N.303 Ligand excluded by PLIP IOD.7: 2 residues within 4Å: Chain B: H.335, Q.341 Ligand excluded by PLIP IOD.8: 5 residues within 4Å: Chain A: P.46, V.47, S.283, P.286, T.287 Ligand excluded by PLIP IOD.9: 1 residues within 4Å: Chain A: Q.361 Ligand excluded by PLIP IOD.18: 2 residues within 4Å: Chain B: K.266, Y.383 Ligand excluded by PLIP IOD.19: 2 residues within 4Å: Chain B: A.55, L.56 Ligand excluded by PLIP IOD.20: 3 residues within 4Å: Chain B: A.234, G.236, G.238 Ligand excluded by PLIP IOD.21: 2 residues within 4Å: Chain B: V.250, P.251 Ligand excluded by PLIP IOD.22: 1 residues within 4Å: Chain B: N.303 Ligand excluded by PLIP IOD.23: 2 residues within 4Å: Chain A: H.335, Q.341 Ligand excluded by PLIP IOD.24: 5 residues within 4Å: Chain B: P.46, V.47, S.283, P.286, T.287 Ligand excluded by PLIP IOD.25: 1 residues within 4Å: Chain B: Q.361 Ligand excluded by PLIP

4 x CL: CHLORIDE ION(Non-functional Binders)

CL.10: 2 residues within 4Å: Chain A: R.79 Chain B: H.335 Ligand excluded by PLIP CL.11: 4 residues within 4Å: Chain A: P.164, A.165, T.166, R.169 Ligand excluded by PLIP CL.26: 2 residues within 4Å: Chain A: H.335 Chain B: R.79 Ligand excluded by PLIP CL.27: 4 residues within 4Å: Chain B: P.164, A.165, T.166, R.169 Ligand excluded by PLIP

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.12: 6 residues within 4Å: Chain A: P.58, E.59, 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.13: 6 residues within 4Å: Chain A: A.63, T.64, H.321, C.322, A.323, E.350 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.63, A:A.323, A:E.350 GOL.14: 5 residues within 4Å: Chain A: F.16, S.17, F.18, D.256, K.257 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:F.18, A:F.18, A:D.256, A:K.257 Water bridges: A:R.15, A:K.257 GOL.15: 2 residues within 4Å: Chain A: E.275, R.276 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.276 Water bridges: A:K.26, A:E.275, A:R.276, A:R.380 GOL.28: 6 residues within 4Å: Chain B: P.58, E.59, 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.29: 6 residues within 4Å: Chain B: A.63, T.64, H.321, C.322, A.323, E.350 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:A.63, B:A.323, B:E.350, B:E.350 GOL.30: 5 residues within 4Å: Chain B: F.16, S.17, F.18, D.256, K.257 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:F.18, B:F.18, B:D.256, B:K.257 Water bridges: B:R.15, B:D.226, B:K.257 GOL.31: 2 residues within 4Å: Chain B: E.275, R.276 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.276 Water bridges: B:K.26, B:E.275, B:E.275, B:R.276, B:R.380

2 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.16: 5 residues within 4Å: Chain A: M.174, M.178, Q.215, S.216, A.219 No protein-ligand interaction detected (PLIP) DMS.32: 5 residues within 4Å: Chain B: M.174, M.178, Q.215, S.216, A.219 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jakobi, S. et al., Hot-spot analysis to dissect the functional protein-protein interface of a tRNA-modifying enzyme. Proteins (2014)

Release Date

2012-11-14

Peptides

Queuine tRNA-ribosyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Queuine tRNA-ribosyltransferase