SMTL ID : 3otb.1

Crystal structure of human tRNAHis guanylyltransferase (Thg1) - dGTP complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.95 Å

Oligo State

homo-tetramer

Ligands

4 x DGT: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

DGT.1: 18 residues within 4Å: Chain A: D.29, G.30, R.31, N.32, F.33, H.34, A.37, F.42, A.43, K.44, P.45, N.46, D.47, S.75, D.76 Ligands: MG.2, MG.3, MG.4 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:R.31, A:N.32, A:F.33, A:H.34, A:A.43, A:A.43, A:D.47, A:S.75 pi-Stacking: A:F.42 DGT.7: 18 residues within 4Å: Chain B: D.29, G.30, R.31, N.32, F.33, H.34, A.37, F.42, A.43, K.44, P.45, N.46, D.47, S.75, D.76 Ligands: MG.8, MG.9, MG.10 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:R.31, B:N.32, B:F.33, B:H.34, B:H.34, B:A.43, B:A.43, B:D.47, B:S.75 pi-Stacking: B:F.42 DGT.11: 18 residues within 4Å: Chain C: D.29, G.30, R.31, N.32, F.33, H.34, A.37, F.42, A.43, K.44, P.45, N.46, D.47, S.75, D.76 Ligands: MG.12, MG.13, MG.14 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:R.31, C:N.32, C:F.33, C:H.34, C:H.34, C:A.43, C:A.43, C:D.47, C:S.75 pi-Stacking: C:F.42 DGT.17: 18 residues within 4Å: Chain D: D.29, G.30, R.31, N.32, F.33, H.34, A.37, F.42, A.43, K.44, P.45, N.46, D.47, S.75, D.76 Ligands: MG.18, MG.19, MG.20 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:R.31, D:N.32, D:F.33, D:H.34, D:A.43, D:A.43, D:D.47, D:S.75 pi-Stacking: D:F.42

12 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.2: 4 residues within 4Å: Chain A: D.29, G.30, D.76 Ligands: DGT.1 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.29, A:G.30, A:D.76 MG.3: 2 residues within 4Å: Ligands: DGT.1, 3PO.6 No protein-ligand interaction detected (PLIP) MG.4: 4 residues within 4Å: Chain A: D.29, S.75, D.76 Ligands: DGT.1 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.29, A:D.76 MG.8: 4 residues within 4Å: Chain B: D.29, G.30, D.76 Ligands: DGT.7 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.29, B:G.30, B:D.76 MG.9: 2 residues within 4Å: Ligands: 3PO.5, DGT.7 No protein-ligand interaction detected (PLIP) MG.10: 4 residues within 4Å: Chain B: D.29, S.75, D.76 Ligands: DGT.7 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.29, B:D.76 MG.12: 4 residues within 4Å: Chain C: D.29, G.30, D.76 Ligands: DGT.11 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.29, C:G.30, C:D.76 MG.13: 2 residues within 4Å: Ligands: DGT.11, 3PO.16 No protein-ligand interaction detected (PLIP) MG.14: 4 residues within 4Å: Chain C: D.29, S.75, D.76 Ligands: DGT.11 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.29, C:D.76 MG.18: 4 residues within 4Å: Chain D: D.29, G.30, D.76 Ligands: DGT.17 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:D.29, D:G.30, D:D.76 MG.19: 2 residues within 4Å: Ligands: 3PO.15, DGT.17 No protein-ligand interaction detected (PLIP) MG.20: 4 residues within 4Å: Chain D: D.29, S.75, D.76 Ligands: DGT.17 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.29, D:D.76

4 x 3PO: TRIPHOSPHATE(Non-covalent)

3PO.5: 5 residues within 4Å: Chain A: R.92, K.95 Chain B: R.27, R.130 Ligands: MG.9 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Salt bridges: A:R.92, A:K.95, B:R.27, B:R.130, B:R.130 3PO.6: 5 residues within 4Å: Chain A: R.27, R.130 Chain B: R.92, K.95 Ligands: MG.3 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Salt bridges: B:R.10, B:R.92, B:K.95, A:R.27, A:R.130, A:R.130 3PO.15: 5 residues within 4Å: Chain C: R.92, K.95 Chain D: R.27, R.130 Ligands: MG.19 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain C Salt bridges: D:R.27, D:R.130, D:R.130, C:R.92, C:K.95 3PO.16: 5 residues within 4Å: Chain C: R.27, R.130 Chain D: R.92, K.95 Ligands: MG.13 6 PLIP interactions: 3 interactions with chain D, 3 interactions with chain C Salt bridges: D:R.10, D:R.92, D:K.95, C:R.27, C:R.130, C:R.130

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hyde, S.J. et al., tRNAHis guanylyltransferase (THG1), a unique 3'-5' nucleotidyl transferase, shares unexpected structural homology with canonical 5'-3' DNA polymerases. Proc.Natl.Acad.Sci.USA (2010)

Release Date

2010-11-17

Peptides

tRNA(His) guanylyltransferase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

tRNA(His) guanylyltransferase

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