SMTL ID : 5axl.1

Crystal structure of Thg1 like protein (TLP) with GTP

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: 18 residues within 4Å: Chain A: D.21, G.22, R.23, N.24, F.25, K.26, L.29, F.34, E.35, K.36, P.37, Y.38, D.39, F.42, S.68, D.69 Ligands: MG.2, MG.3 11 PLIP interactions: 9 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:G.22, A:N.24, A:F.25, A:K.26, A:E.35, A:E.35, A:D.39 Water bridges: A:S.68, A:S.68, B:K.86, B:K.86 GTP.4: 14 residues within 4Å: Chain B: D.21, G.22, R.23, N.24, F.25, E.35, P.37, Y.38, D.39, F.42, S.68, D.69 Ligands: MG.5, MG.6 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:N.24, B:F.25, B:E.35, B:E.35, B:D.39 Water bridges: B:D.21, B:S.68, B:N.137 GTP.7: 18 residues within 4Å: Chain C: D.21, G.22, R.23, N.24, F.25, K.26, L.29, F.34, E.35, K.36, P.37, Y.38, D.39, F.42, S.68, D.69 Ligands: MG.8, MG.9 11 PLIP interactions: 9 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:G.22, C:N.24, C:F.25, C:K.26, C:E.35, C:E.35, C:D.39 Water bridges: C:S.68, C:S.68, D:K.86, D:K.86 GTP.10: 14 residues within 4Å: Chain D: D.21, G.22, R.23, N.24, F.25, E.35, P.37, Y.38, D.39, F.42, S.68, D.69 Ligands: MG.11, MG.12 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:N.24, D:F.25, D:E.35, D:E.35, D:D.39 Water bridges: D:D.21, D:S.68, D:N.137

8 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: D.21, G.22, D.69 Ligands: GTP.1, MG.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.21, A:G.22, A:D.69 MG.3: 4 residues within 4Å: Chain A: D.21, D.69 Ligands: GTP.1, MG.2 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.21, A:D.69, H2O.1, H2O.1 MG.5: 5 residues within 4Å: Chain B: D.21, G.22, D.69 Ligands: GTP.4, MG.6 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.21, B:G.22, B:D.69 MG.6: 6 residues within 4Å: Chain B: D.21, S.68, D.69, E.70 Ligands: GTP.4, MG.5 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.21, B:D.69, H2O.1, H2O.1 MG.8: 5 residues within 4Å: Chain C: D.21, G.22, D.69 Ligands: GTP.7, MG.9 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.21, C:G.22, C:D.69 MG.9: 4 residues within 4Å: Chain C: D.21, D.69 Ligands: GTP.7, MG.8 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.21, C:D.69, H2O.1, H2O.1 MG.11: 5 residues within 4Å: Chain D: D.21, G.22, D.69 Ligands: GTP.10, MG.12 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:D.21, D:G.22, D:D.69 MG.12: 6 residues within 4Å: Chain D: D.21, S.68, D.69, E.70 Ligands: GTP.10, MG.11 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.21, D:D.69, H2O.1, H2O.1

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kimura, S. et al., Template-dependent nucleotide addition in the reverse (3'-5') direction by Thg1-like protein. Sci Adv (2016)

Release Date

2016-08-03

Peptides

tRNA(His)-5'-guanylyltransferase (Thg1) like protein: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

tRNA(His)-5'-guanylyltransferase (Thg1) like protein

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