SMTL ID : 6l3g.1

Structural Basis for DNA Unwinding at Forked dsDNA by two coordinating Pif1 helicases

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.30 Å

Oligo State

homo-tetramer

Ligands

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

ADP.1: 16 residues within 4Å: Chain B: M.4, I.5, A.30, G.31, S.32, G.33, K.34, T.35, T.36, F.187, R.188, G.365, T.367, R.392 Ligands: MG.2, ALF.3 19 PLIP interactions: 19 interactions with chain B Hydrogen bonds: B:I.5, B:I.5, B:G.31, B:S.32, B:S.32, B:G.33, B:K.34, B:T.35, B:T.35, B:T.36, B:T.36, B:T.367, B:R.392, B:R.392 Salt bridges: B:K.34, B:R.188, B:R.188 pi-Stacking: B:F.187, B:F.187 ADP.4: 17 residues within 4Å: Chain C: D.3, M.4, I.5, A.30, G.31, S.32, G.33, K.34, T.35, T.36, F.187, R.188, G.365, T.367, R.392 Ligands: MG.5, ALF.6 17 PLIP interactions: 17 interactions with chain C Hydrogen bonds: C:I.5, C:I.5, C:G.31, C:S.32, C:G.33, C:K.34, C:T.35, C:T.36, C:N.61, C:T.367, C:R.392, C:R.392 Salt bridges: C:K.34, C:R.188, C:R.188 pi-Stacking: C:F.187, C:F.187 ADP.7: 16 residues within 4Å: Chain E: M.4, I.5, A.30, G.31, S.32, G.33, K.34, T.35, T.36, F.187, R.188, G.365, T.367, R.392 Ligands: MG.8, ALF.9 20 PLIP interactions: 20 interactions with chain E Hydrogen bonds: E:I.5, E:I.5, E:G.31, E:S.32, E:S.32, E:G.33, E:K.34, E:T.35, E:T.35, E:T.36, E:T.36, E:T.367, E:T.367, E:R.392, E:R.392 Salt bridges: E:K.34, E:R.188, E:R.188 pi-Stacking: E:F.187, E:F.187 ADP.10: 17 residues within 4Å: Chain F: D.3, M.4, I.5, A.30, G.31, S.32, G.33, K.34, T.35, T.36, F.187, R.188, G.365, T.367, R.392 Ligands: MG.11, ALF.12 17 PLIP interactions: 17 interactions with chain F Hydrogen bonds: F:I.5, F:I.5, F:G.31, F:S.32, F:G.33, F:K.34, F:T.35, F:T.36, F:T.36, F:N.61, F:R.392, F:R.392 Salt bridges: F:K.34, F:R.188, F:R.188 pi-Stacking: F:F.187, F:F.187

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain B: T.35, E.106 Ligands: ADP.1, ALF.3 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:T.35, H2O.1 MG.5: 3 residues within 4Å: Chain C: T.35 Ligands: ADP.4, ALF.6 2 PLIP interactions: 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:T.35, H2O.1 MG.8: 4 residues within 4Å: Chain E: T.35, E.106 Ligands: ADP.7, ALF.9 2 PLIP interactions: 1 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:T.35, H2O.1 MG.11: 3 residues within 4Å: Chain F: T.35 Ligands: ADP.10, ALF.12 2 PLIP interactions: 1 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:T.35, H2O.1

4 x ALF: TETRAFLUOROALUMINATE ION(Non-covalent)

ALF.3: 11 residues within 4Å: Chain B: A.30, G.31, K.34, T.35, E.106, Q.145, R.188, G.365, R.390 Ligands: ADP.1, MG.2 No protein-ligand interaction detected (PLIP) ALF.6: 11 residues within 4Å: Chain C: A.30, G.31, K.34, T.35, E.106, Q.145, R.188, G.365, R.390 Ligands: ADP.4, MG.5 No protein-ligand interaction detected (PLIP) ALF.9: 11 residues within 4Å: Chain E: A.30, G.31, K.34, T.35, E.106, Q.145, R.188, G.365, R.390 Ligands: ADP.7, MG.8 No protein-ligand interaction detected (PLIP) ALF.12: 11 residues within 4Å: Chain F: A.30, G.31, K.34, T.35, E.106, Q.145, R.188, G.365, R.390 Ligands: ADP.10, MG.11 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Su, N. et al., Structural basis for DNA unwinding at forked dsDNA by two coordinating Pif1 helicases. Nat Commun (2019)

Release Date

2019-12-11

Peptides

ATP-dependent DNA helicase: BCEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

B
A

C
B

E
A

F
B

ATP-dependent DNA helicase

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