SMTL ID : 7bil.1

Crystal structure of helicase Pif1 from Thermus oshimai in complex with oligo GGTTTGGTTTGGTT

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.21 Å

Oligo State

homo-dimer

Ligands

2 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.1: 17 residues within 4Å: Chain A: G.67, L.68, S.69, Q.72, A.93, G.94, T.95, G.96, K.97, T.98, T.99, Q.255, R.256, R.258, T.438 Ligands: MG.2, ALF.3 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:S.69, A:Q.72, A:Q.72, A:G.94, A:T.95, A:G.96, A:K.97, A:T.98, A:T.98, A:T.99, A:T.99, A:R.258, A:T.438, A:T.438 Water bridges: A:T.98, A:R.462, A:R.464 Salt bridges: A:K.97, A:R.256, A:R.256 ADP.5: 16 residues within 4Å: Chain B: G.67, L.68, S.69, Q.72, G.94, T.95, G.96, K.97, T.98, T.99, Q.255, R.256, R.258, T.438 Ligands: MG.6, ALF.7 19 PLIP interactions: 19 interactions with chain B Hydrogen bonds: B:S.69, B:Q.72, B:Q.72, B:G.94, B:T.95, B:T.95, B:G.96, B:K.97, B:T.98, B:T.99, B:T.99, B:R.258, B:T.438 Water bridges: B:T.98, B:Q.124, B:E.172 Salt bridges: B:K.97, B:R.256, B:R.256

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: T.98, D.171, E.172 Ligands: ADP.1, ALF.3 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:T.98, H2O.2, H2O.2, H2O.3 MG.6: 5 residues within 4Å: Chain B: T.98, D.171, E.172 Ligands: ADP.5, ALF.7 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:T.98, H2O.4, H2O.4, H2O.4

2 x ALF: TETRAFLUOROALUMINATE ION(Non-covalent)

ALF.3: 10 residues within 4Å: Chain A: A.93, G.94, K.97, E.172, Q.212, R.256, G.436, R.462 Ligands: ADP.1, MG.2 No protein-ligand interaction detected (PLIP) ALF.7: 11 residues within 4Å: Chain B: A.93, G.94, K.97, T.98, E.172, Q.212, R.256, G.436, R.462 Ligands: ADP.5, MG.6 No protein-ligand interaction detected (PLIP)

1 x K: POTASSIUM ION(Non-covalent)

K.4: 2 residues within 4Å: Chain A: K.109, R.111 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dai, Y.X. et al., Structural and functional studies of SF1B Pif1 from Thermus oshimai reveal dimerization-induced helicase inhibition. Nucleic Acids Res. (2021)

Release Date

2021-04-07

Peptides

PIF1 helicase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

PIF1 helicase