SMTL ID : 6yhd.1

tRNA-guanine Transglycosylase (TGT) labeled with 5-fluorotryptophan in co-crystallized complex with 6-amino-4-(2-((2R,3S,4R,5R)-3,4-dihydroxy-5-methoxytetrahydrofuran-2-yl)ethyl)-2-(methylamino)-3,7-dihydro-8H-imidazo[4,5-g]quinazolin-8-one

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.25 Å

Oligo State

homo-dimer

Ligands

2 x 1WK: methyl 6-[6-amino-2-(methylamino)-8-oxo-7,8-dihydro-1H-imidazo[4,5-g]quinazolin-4-yl]-5,6-dideoxy-beta-D-ribo-hexofuranoside(Non-covalent)

1WK.1: 22 residues within 4Å: Chain A: V.47, T.49, L.70, N.72, H.75, D.104, S.105, G.107, Y.108, Q.109, D.158, C.160, I.203, Q.205, G.231, G.232, L.233, A.234, V.235, M.262, G.263, D.282 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:Y.108, A:Y.108 Hydrogen bonds: A:N.72, A:S.105, A:Y.108, A:Q.109, A:Q.205, A:G.232, A:L.233, A:A.234, A:D.282 Water bridges: A:G.106, A:Y.108, A:M.262 Salt bridges: A:H.75, A:D.104, A:D.158 1WK.6: 22 residues within 4Å: Chain B: V.47, T.49, L.70, N.72, H.75, D.104, S.105, G.107, Y.108, Q.109, D.158, C.160, I.203, Q.205, G.231, G.232, L.233, A.234, V.235, M.262, G.263, D.282 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:Y.108, B:Y.108 Hydrogen bonds: B:N.72, B:S.105, B:Y.108, B:Q.109, B:Q.205, B:G.232, B:L.233, B:A.234, B:D.282 Water bridges: B:G.106, B:Y.108, B:M.262 Salt bridges: B:H.75, B:D.104, B:D.158

4 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 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain A Water bridges: B:K.327, A:R.99 Hydrogen bonds: A:G.96, A:D.98, A:R.99 GOL.3: 7 residues within 4Å: Chain A: W.298, E.319, K.362, F.375, D.378, F.379, R.382 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.319, A:K.362, A:D.378, A:R.382 Water bridges: A:E.319 GOL.7: 7 residues within 4Å: Chain B: P.58, E.59, R.62, G.96, W.97, D.98, R.99 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:G.96, B:D.98, B:R.99 Water bridges: B:R.99, A:K.327 GOL.8: 7 residues within 4Å: Chain B: W.298, E.319, K.362, F.375, D.378, F.379, R.382 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.319, B:K.362, B:D.378, B:R.382

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

CL.4: 5 residues within 4Å: Chain A: K.54, V.284, T.287, R.288, R.291 Ligand excluded by PLIP CL.9: 5 residues within 4Å: Chain B: K.54, V.284, T.287, R.288, R.291 Ligand excluded by PLIP

2 x ZN: ZINC ION(Non-covalent)

ZN.5: 5 residues within 4Å: Chain A: C.320, C.322, V.324, 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.10: 5 residues within 4Å: Chain B: C.320, C.322, V.324, 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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nguyen, A. et al., Co-crystallization, nanoESI-MS and 19F NMR reveal dimer disturbing inhibitors and conformational changes at dimer contacts. To Be Published

Release Date

2020-04-08

Peptides

Queuine tRNA-ribosyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Queuine tRNA-ribosyltransferase

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