SMTL ID : 3wbz.1 (1 other biounit)

Crystal structure of C. albicans tRNA(His) guanylyltransferase (Thg1) with ATP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.39 Å

Oligo State

homo-tetramer

Ligands

8 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.1: 19 residues within 4Å: Chain A: D.32, G.33, K.34, G.35, F.36, H.37, S.40, F.45, E.46, K.47, P.48, N.49, D.50, A.53, L.54, S.78, D.79 Ligands: MG.3, MG.4 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:D.32, A:G.35, A:F.36, A:H.37, A:K.47, A:D.50, A:D.50 Water bridges: A:G.33, A:K.38, A:S.78 pi-Stacking: A:F.45 ATP.2: 10 residues within 4Å: Chain A: R.30, R.135, W.151, R.152, D.155 Chain B: E.10, K.13, R.95, K.98 Ligands: MG.5 21 PLIP interactions: 10 interactions with chain A, 11 interactions with chain B Hydrogen bonds: A:R.152, A:R.152, A:D.155 Water bridges: A:D.133, A:R.135, A:R.135, A:R.135, B:K.13, B:K.13, B:R.95, B:R.95, B:K.98, B:K.98 Salt bridges: A:R.30, A:R.135, A:R.135, B:K.13, B:K.13, B:R.95, B:K.98 pi-Cation interactions: B:K.13 ATP.6: 19 residues within 4Å: Chain B: D.32, G.33, K.34, G.35, F.36, H.37, S.40, F.45, E.46, K.47, P.48, N.49, D.50, A.53, L.54, S.78, D.79 Ligands: MG.8, MG.9 17 PLIP interactions: 16 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:G.35, B:F.36, B:H.37, B:H.37, B:K.47, B:D.50, B:D.50 Water bridges: B:D.32, B:G.33, B:K.34, B:G.35, B:K.38, B:D.133, A:K.98 Salt bridges: B:H.37, B:H.37 pi-Stacking: B:F.45 ATP.7: 9 residues within 4Å: Chain A: K.13, R.95, K.98 Chain B: R.30, R.135, W.151, R.152, D.155 Ligands: MG.10 14 PLIP interactions: 6 interactions with chain B, 8 interactions with chain A Hydrogen bonds: B:D.155 Water bridges: B:R.30, B:R.30, A:K.98, A:K.98, A:K.98, A:K.98 Salt bridges: B:R.30, B:R.135, B:R.135, A:K.13, A:R.95, A:K.98 pi-Cation interactions: A:K.13 ATP.11: 20 residues within 4Å: Chain C: D.32, G.33, K.34, G.35, F.36, H.37, S.40, F.45, E.46, K.47, P.48, N.49, D.50, A.53, L.54, S.78, D.79 Ligands: MG.13, MG.14, MG.15 14 PLIP interactions: 14 interactions with chain C Hydrogen bonds: C:G.35, C:F.36, C:H.37, C:S.40, C:K.47, C:D.50, C:D.50, C:L.54 Water bridges: C:D.32, C:G.33, C:S.78 Salt bridges: C:H.37, C:H.37 pi-Stacking: C:F.45 ATP.12: 10 residues within 4Å: Chain C: R.30, R.135, W.151, R.152, D.155 Chain D: E.10, K.13, R.95, K.98 Ligands: MG.15 22 PLIP interactions: 8 interactions with chain C, 14 interactions with chain D Hydrogen bonds: C:R.152, C:D.155 Water bridges: C:R.30, C:R.30, C:R.135, D:K.13, D:R.95, D:R.95, D:R.95, D:K.98, D:K.98, D:K.98, D:K.98 Salt bridges: C:R.30, C:R.135, C:R.135, D:K.13, D:K.13, D:K.13, D:R.95, D:K.98 pi-Cation interactions: D:K.13 ATP.16: 19 residues within 4Å: Chain D: D.32, G.33, K.34, G.35, F.36, H.37, S.40, F.45, E.46, K.47, P.48, N.49, D.50, A.53, L.54, S.78, D.79 Ligands: MG.18, MG.19 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:G.35, D:F.36, D:H.37, D:K.47, D:D.50, D:D.50 Water bridges: D:G.33, D:K.34, D:K.38 pi-Stacking: D:F.45 ATP.17: 10 residues within 4Å: Chain C: E.10, K.13, R.95, K.98 Chain D: R.30, R.135, W.151, R.152, D.155 Ligands: MG.20 19 PLIP interactions: 9 interactions with chain C, 10 interactions with chain D Water bridges: C:K.13, C:K.98, C:K.98, C:K.98, D:R.30, D:R.30, D:R.135, D:R.135 Salt bridges: C:K.13, C:K.13, C:R.95, C:K.98, D:R.30, D:R.135, D:R.135 pi-Cation interactions: C:K.13 Hydrogen bonds: D:R.152, D:R.152, D:D.155

12 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: D.32, D.79 Ligands: ATP.1, MG.4 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.32, A:D.79, H2O.2, H2O.3, H2O.3 MG.4: 5 residues within 4Å: Chain A: D.32, G.33, D.79 Ligands: ATP.1, MG.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.32, A:G.33, A:D.79 MG.5: 3 residues within 4Å: Chain A: R.135 Chain B: K.98 Ligands: ATP.2 No protein-ligand interaction detected (PLIP) MG.8: 4 residues within 4Å: Chain B: D.32, D.79 Ligands: ATP.6, MG.9 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.32, B:D.79, H2O.4, H2O.5, H2O.5 MG.9: 5 residues within 4Å: Chain B: D.32, G.33, D.79 Ligands: ATP.6, MG.8 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.32, B:G.33, B:D.79 MG.10: 2 residues within 4Å: Chain B: R.135 Ligands: ATP.7 No protein-ligand interaction detected (PLIP) MG.13: 4 residues within 4Å: Chain C: D.32, D.79 Ligands: ATP.11, MG.14 5 PLIP interactions: 2 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:D.32, C:D.79, H2O.7, H2O.7, H2O.7 MG.14: 5 residues within 4Å: Chain C: D.32, G.33, D.79 Ligands: ATP.11, MG.13 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.32, C:G.33, C:D.79 MG.15: 4 residues within 4Å: Chain C: R.135 Chain D: K.98 Ligands: ATP.11, ATP.12 No protein-ligand interaction detected (PLIP) MG.18: 4 residues within 4Å: Chain D: D.32, D.79 Ligands: ATP.16, MG.19 5 PLIP interactions: 2 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:D.32, D:D.79, H2O.8, H2O.9, H2O.9 MG.19: 5 residues within 4Å: Chain D: D.32, G.33, D.79 Ligands: ATP.16, MG.18 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:D.32, D:G.33, D:D.79 MG.20: 2 residues within 4Å: Chain C: K.98 Ligands: ATP.17 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nakamura, A. et al., Structural basis of reverse nucleotide polymerization. Proc.Natl.Acad.Sci.USA (2013)

Release Date

2013-12-18

Peptides

Likely histidyl tRNA-specific guanylyltransferase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Likely histidyl tRNA-specific guanylyltransferase

Related Entries With Identical Sequence