SMTL ID : 5xox.1 (1 other biounit)

Crystal structure of tRNA(His) guanylyltranserase from Saccharomyces cerevisiae

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

homo-tetramer

Ligands

4 x GTP: GUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

GTP.1: 17 residues within 4Å: Chain A: D.29, G.30, K.31, K.32, F.33, H.34, S.37, F.42, A.43, K.44, N.46, D.47, L.51, S.76, D.77 Ligands: MG.2, MG.3 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:K.32, A:F.33, A:H.34, A:H.34, A:S.37, A:A.43, A:K.44, A:D.47 Salt bridges: A:K.32, A:K.32 GTP.6: 15 residues within 4Å: Chain B: D.29, G.30, K.31, K.32, F.33, H.34, S.37, F.42, K.44, N.46, D.47, L.51, S.76, D.77 Ligands: MG.8 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:K.32, B:F.33, B:H.34, B:H.34, B:S.37, B:F.42, B:K.44, B:K.44, B:D.47 Salt bridges: B:K.32 pi-Stacking: B:F.42 GTP.9: 17 residues within 4Å: Chain C: D.29, G.30, K.31, K.32, F.33, H.34, S.37, F.42, K.44, N.46, D.47, A.50, L.51, S.76, D.77 Ligands: MG.10, MG.11 10 PLIP interactions: 1 interactions with chain D, 9 interactions with chain C Salt bridges: D:K.96, C:K.31, C:K.32 Hydrogen bonds: C:K.32, C:F.33, C:H.34, C:H.34, C:S.37, C:D.47 pi-Stacking: C:F.42 GTP.14: 16 residues within 4Å: Chain D: D.29, G.30, K.32, F.33, H.34, S.37, F.42, K.44, P.45, N.46, D.47, L.51, S.76, D.77 Ligands: MG.15, MG.16 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:K.32, D:F.33, D:H.34, D:H.34, D:S.37, D:S.37, D:K.44, D:K.44, D:D.47

8 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: D.29, D.77, E.78 Ligands: GTP.1 No protein-ligand interaction detected (PLIP) MG.3: 4 residues within 4Å: Chain A: D.29, G.30, D.77 Ligands: GTP.1 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.29, A:G.30 MG.7: 3 residues within 4Å: Chain B: E.75, E.78, D.153 No protein-ligand interaction detected (PLIP) MG.8: 4 residues within 4Å: Chain B: D.29, G.30, D.77 Ligands: GTP.6 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.29, B:G.30, B:D.77 MG.10: 2 residues within 4Å: Chain C: D.29 Ligands: GTP.9 No protein-ligand interaction detected (PLIP) MG.11: 4 residues within 4Å: Chain C: D.29, G.30, D.77 Ligands: GTP.9 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.29, C:G.30 MG.15: 5 residues within 4Å: Chain D: D.29, E.75, D.77, E.78 Ligands: GTP.14 No protein-ligand interaction detected (PLIP) MG.16: 4 residues within 4Å: Chain D: D.29, G.30, D.77 Ligands: GTP.14 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:D.29, D:G.30, D:D.77

4 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.4: 4 residues within 4Å: Chain A: H.15, R.93, K.96 Chain B: R.133 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Salt bridges: A:H.15, A:R.93, A:K.96, B:R.133 PO4.5: 4 residues within 4Å: Chain A: R.133 Chain B: H.15, R.93, K.96 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Salt bridges: A:R.133, B:H.15, B:R.93, B:K.96 PO4.12: 4 residues within 4Å: Chain C: R.10, R.93, K.96 Chain D: R.133 4 PLIP interactions: 1 interactions with chain D, 3 interactions with chain C Salt bridges: D:R.133, C:R.10, C:R.93, C:K.96 PO4.13: 5 residues within 4Å: Chain C: R.133 Chain D: R.10, H.15, R.93, K.96 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain C Salt bridges: D:R.10, D:R.93, D:K.96, C:R.133

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lee, K. et al., Crystal structure of tRNA(His) guanylyltransferase from Saccharomyces cerevisiae. Biochem. Biophys. Res. Commun. (2017)

Release Date

2017-07-12

Peptides

tRNA(His) guanylyltransferase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

tRNA(His) guanylyltransferase

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