SMTL ID : 7ovo.1

Heterodimeric murine tRNA-guanine transglycosylase in complex with queuine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

hetero-1-1-mer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.352, C.354, C.357, H.383 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.352, A:C.354, A:C.357, A:H.383 ZN.6: 4 residues within 4Å: Chain B: C.309, C.311, C.314, H.340 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.309, B:C.311, B:C.314, B:H.340

7 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 5 residues within 4Å: Chain A: K.339, Q.342, H.366, M.370 Chain B: R.72 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Water bridges: B:R.72 Salt bridges: B:R.72, A:H.366 SO4.3: 4 residues within 4Å: Chain A: L.234, H.235, S.238, R.267 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.238, A:S.238 Salt bridges: A:H.235, A:R.267 SO4.7: 3 residues within 4Å: Chain B: P.380, A.381, W.382 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:A.381, B:W.382 SO4.8: 2 residues within 4Å: Chain B: K.295, K.296 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.296 SO4.9: 3 residues within 4Å: Chain B: A.5, P.6, R.7 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.7, B:R.7 SO4.10: 1 residues within 4Å: Chain B: H.68 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:H.68 SO4.11: 6 residues within 4Å: Chain B: N.290, L.291, Q.292, K.295, Q.297, Y.298 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.292, B:Q.292, B:Q.297, B:Y.298

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

DMS.4: 6 residues within 4Å: Chain A: H.45, L.46, T.47, V.378 Chain B: T.332, H.335 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:H.45 Water bridges: A:S.42 pi-Cation interactions: B:H.335, B:H.336

1 x QEI: 2-amino-5-({[(1S,4S,5R)-4,5-dihydroxycyclopent-2-en-1-yl]amino}methyl)-3,7-dihydro-4H-pyrrolo[2,3-d]pyrimidin-4-one(Non-covalent)

QEI.5: 15 residues within 4Å: Chain B: F.101, Q.102, D.151, V.153, V.154, S.155, S.156, I.192, Q.194, G.220, G.221, L.222, S.223, G.224, M.251 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:V.153, B:M.251 Hydrogen bonds: B:Q.102, B:S.156, B:Q.194, B:G.221, B:L.222 Water bridges: B:S.98, B:S.98, B:S.98, B:L.222, B:L.222, B:S.223 Salt bridges: B:D.151 pi-Stacking: B:F.101, B:F.101

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sebastiani, M. et al., Structural and Biochemical Investigation of the Heterodimeric Murine tRNA-Guanine Transglycosylase. Acs Chem.Biol. (2022)

Release Date

2022-06-22

Peptides

Queuine tRNA-ribosyltransferase accessory subunit 2: A
Queuine tRNA-ribosyltransferase catalytic subunit 1: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

Queuine tRNA-ribosyltransferase accessory subunit 2

Queuine tRNA-ribosyltransferase catalytic subunit 1

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