SMTL ID : 6ygx.1

tRNA-guanine Transglycosylase (TGT) labeled with 5-fluorotryptophan in co-crystallized complex with 6-amino-2-(methylamino)-4-(2-((2R,3R,4S,5R,6S)-3,4,5,6-tetramethoxytetrahydro-2H-pyran-2-yl)ethyl)-1H-imidazo[4,5-g]quinazolin-8(7H)-one

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.35 Å

Oligo State

homo-dimer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 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.3: 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

2 x 726: 6-azanyl-2-(methylamino)-4-[2-[(2~{R},3~{R},4~{S},5~{R},6~{S})-3,4,5,6-tetramethoxyoxan-2-yl]ethyl]-1,7-dihydroimidazo[4,5-g]quinazolin-8-one(Non-covalent)

726.2: 22 residues within 4Å: Chain A: V.47, L.70, N.72, L.102, D.104, S.105, Y.108, Q.109, D.158, C.160, I.203, Q.205, G.231, G.232, L.233, A.234, V.235, Y.260, M.262, G.263, D.282, V.284 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:Y.108, A:M.262 Hydrogen bonds: A:S.105, A:Q.205, A:G.232, A:L.233, A:A.234 Water bridges: A:N.72, A:Y.108, A:Q.109, A:D.158, A:C.160 Salt bridges: A:D.104, A:D.158 pi-Stacking: A:Y.108 726.4: 22 residues within 4Å: Chain B: V.47, L.70, N.72, L.102, D.104, S.105, Y.108, Q.109, D.158, C.160, I.203, Q.205, G.231, G.232, L.233, A.234, V.235, Y.260, M.262, G.263, D.282, V.284 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:Y.108, B:M.262 Hydrogen bonds: B:D.104, B:S.105, B:Q.205, B:G.232, B:L.233, B:A.234 Water bridges: B:N.72, B:Y.108, B:Q.109, B:D.158, B:C.160, B:D.282 Salt bridges: B:D.104, B:D.158 pi-Stacking: B:Y.108

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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