SMTL ID : 7a3v.1

tRNA-guanine transglycosylase C158S/C281S/Y330C/H333A mutant in complex with 3-hydroxysulfolane

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.7: 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

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 3 residues within 4Å: Chain A: R.36, D.98, R.99 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.99, A:R.99 GOL.3: 4 residues within 4Å: Chain A: R.40, R.62, A.63, G.65 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.40, A:R.40, A:R.62, A:G.65 Water bridges: A:R.62 GOL.8: 3 residues within 4Å: Chain B: R.36, D.98, R.99 2 PLIP interactions: 2 interactions with chain B Water bridges: B:R.99, B:R.99 GOL.9: 4 residues within 4Å: Chain B: R.40, R.62, A.63, G.65 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.40, B:R.40, B:R.62, B:G.65 Water bridges: B:R.62

4 x QXE: 3-hydroxythietane-1,1-dioxide(Non-covalent)

QXE.4: 6 residues within 4Å: Chain A: G.48, L.56, P.58, V.61, M.95, W.97 2 PLIP interactions: 2 interactions with chain A Water bridges: A:L.56, A:M.95 QXE.5: 5 residues within 4Å: Chain A: M.77, G.81, A.82, E.83, H.135 No protein-ligand interaction detected (PLIP) QXE.10: 6 residues within 4Å: Chain B: G.48, L.56, P.58, V.61, M.95, W.97 2 PLIP interactions: 2 interactions with chain B Water bridges: B:L.56, B:M.95 QXE.11: 5 residues within 4Å: Chain B: M.77, G.81, A.82, E.83, H.135 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.135

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.6: 6 residues within 4Å: Chain A: G.107, F.157, D.158, E.159, S.160, W.180 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.160, A:S.160 EDO.12: 6 residues within 4Å: Chain B: G.107, F.157, D.158, E.159, S.160, W.180 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.160, B:S.160

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nguyen, D. et al., Targeting a Cryptic Pocket in a Protein-Protein Contact by Disulfide-Induced Rupture of a Homodimeric Interface. Acs Chem.Biol. (2021)

Release Date

2021-06-16

Peptides

Queuine tRNA-ribosyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Queuine tRNA-ribosyltransferase

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