SMTL ID : 7b2i.1

Heterodimeric tRNA-Guanine Transglycosylase from mouse

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 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

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

SO4.2: 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:L.234, A:S.238 Salt bridges: A:H.235, A:R.267 SO4.3: 4 residues within 4Å: Chain A: Q.342, H.366, M.370 Chain B: R.120 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:E.111 Salt bridges: B:R.120, A:H.366 SO4.7: 1 residues within 4Å: Chain B: H.327 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:H.327 SO4.8: 3 residues within 4Å: Chain B: R.17, P.362, R.366 4 PLIP interactions: 4 interactions with chain B Water bridges: B:D.363, B:R.366 Salt bridges: B:R.17, B:R.366

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.4: 8 residues within 4Å: Chain A: H.45, T.281, E.282, L.369, N.372, E.373, L.374, G.377 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.282 PEG.10: 5 residues within 4Å: Chain B: T.31, V.32, A.33, V.36, R.60 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:A.33

2 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.5: 12 residues within 4Å: Chain A: E.282, R.283, G.284, K.337, L.369, M.370, N.372 Chain B: L.106, E.111, V.158, T.159, L.162 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:E.111, A:K.337 Water bridges: B:T.159, A:N.335 PG4.11: 8 residues within 4Å: Chain B: P.287, N.306, Q.347, L.348, F.364, N.367, F.368, T.371 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.306

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.9: 13 residues within 4Å: Chain B: G.41, T.42, T.45, I.49, T.50, T.51, L.54, C.62, L.63, G.64, M.88, W.90, L.94 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:G.41, B:T.42, B:I.49, B:L.63 Water bridges: B:T.51

1 x P6G: HEXAETHYLENE GLYCOL(Non-functional Binders)

P6G.12: 7 residues within 4Å: Chain B: R.7, I.8, M.9, R.10, E.24, R.26, T.31 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.26

1 x CIT: CITRIC ACID(Non-functional Binders)

CIT.13: 11 residues within 4Å: Chain B: Q.102, D.151, V.153, I.192, Q.194, G.220, G.221, L.222, S.223, M.251, G.252 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:Q.194, B:G.221, B:L.222, B:S.223, B:S.223, B:M.251 Water bridges: B:Q.102, B:D.151, B:G.220, B:M.251

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

2021-12-08

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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