SMTL ID : 7oar.1

Crystal structure of helicase Pif1 from Thermus oshimai in complex with parallel G-quadruplex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.58 Å

Oligo State

homo-dimer

Ligands

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

ADP.1: 17 residues within 4Å: Chain A: E.7, G.8, L.9, S.10, Q.13, G.35, T.36, G.37, K.38, T.39, T.40, Q.196, R.197, R.199, T.379 Ligands: MG.2, ALF.3 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:G.8, A:S.10, A:Q.13, A:G.35, A:T.36, A:G.37, A:K.38, A:T.39, A:T.40, A:T.40, A:R.199, A:G.377, A:T.379, A:T.379 Water bridges: A:T.39 Salt bridges: A:K.38, A:R.197, A:R.197 ADP.4: 16 residues within 4Å: Chain B: G.8, L.9, S.10, Q.13, G.35, T.36, G.37, K.38, T.39, T.40, Q.196, R.197, R.199, T.379 Ligands: MG.5, ALF.6 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:S.10, B:Q.13, B:Q.13, B:G.35, B:T.36, B:G.37, B:K.38, B:T.39, B:T.40, B:T.40, B:T.379 Water bridges: B:R.197 Salt bridges: B:K.38, B:R.197, B:R.197

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: T.39, D.112 Ligands: ADP.1, ALF.3 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:T.39, H2O.1, H2O.1, H2O.1 MG.5: 5 residues within 4Å: Chain B: T.39, D.112, E.113 Ligands: ADP.4, ALF.6 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:T.39, H2O.2, H2O.2

2 x ALF: TETRAFLUOROALUMINATE ION(Non-covalent)

ALF.3: 11 residues within 4Å: Chain A: A.34, G.35, K.38, T.39, E.113, Q.153, R.197, G.377, R.403 Ligands: ADP.1, MG.2 No protein-ligand interaction detected (PLIP) ALF.6: 10 residues within 4Å: Chain B: A.34, G.35, K.38, E.113, Q.153, R.197, G.377, R.403 Ligands: ADP.4, MG.5 No protein-ligand interaction detected (PLIP)

3 x K: POTASSIUM ION(Non-functional Binders)

K.7: 9 residues within 4Å: Chain C: G.7, G.8, G.11, G.12, G.15, G.16, G.19, G.20 Ligands: K.8 No protein-ligand interaction detected (PLIP) K.8: 9 residues within 4Å: Chain C: G.8, G.9, G.12, G.13, G.16, G.17, G.20, G.21 Ligands: K.7 No protein-ligand interaction detected (PLIP) K.9: 3 residues within 4Å: Chain C: G.13, G.17, T.22 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dai, Y.X. et al., Structural mechanism underpinning Thermus oshimai Pif1-mediated G-quadruplex unfolding. Embo Rep. (2022)

Release Date

2022-03-09

Peptides

Pif1 helicase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Pif1 helicase