SMTL ID : 5o6b.1

Structure of ScPif1 in complex with GGGTTTT and ADP-AlF4

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.03 Å

Oligo State

homo-dimer

Ligands

2 x DG- DG- DG- DT- DT- DT: DNA (5'-D(*GP*GP*GP*TP*TP*T)-3')(Non-covalent)

DG-DG-DG-DT-DT-DT.1: 27 residues within 4Å: Chain A: S.54, T.55, G.56, T.66, H.68, S.69, G.74, L.75, V.150, S.151, K.152, S.228, T.229, R.230, N.271, L.273, N.291, N.298, S.468, H.470, K.471, F.488, E.489 Chain B: T.229, R.267, R.486 Ligands: DG-DG-DG-DT-DT-DT.2 Protein-ligand interaction information (PLIP) not available DG-DG-DG-DT-DT-DT.2: 28 residues within 4Å: Chain A: T.229, E.263, R.486 Chain B: S.54, T.55, G.56, T.66, H.68, S.69, G.74, L.75, K.77, V.150, S.151, K.152, S.228, T.229, R.230, K.290, N.291, N.298, E.446, S.468, H.470, K.471, F.488, E.489 Ligands: DG-DG-DG-DT-DT-DT.1 Protein-ligand interaction information (PLIP) not available

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

ADP.3: 16 residues within 4Å: Chain A: G.1, L.2, S.3, Q.6, G.26, T.27, G.28, K.29, S.30, I.31, F.181, R.182, R.184, T.476 Ligands: ALF.4, MG.5 25 PLIP interactions: 25 interactions with chain A Hydrogen bonds: A:S.3, A:Q.6, A:Q.6, A:G.26, A:T.27, A:T.27, A:G.28, A:K.29, A:S.30, A:I.31, A:T.476 Water bridges: A:G.1, A:S.30, A:S.30, A:N.61, A:N.61, A:R.184, A:R.184, A:T.476, A:R.499 Salt bridges: A:K.29, A:R.182, A:R.182 pi-Stacking: A:F.181, A:F.181 ADP.6: 13 residues within 4Å: Chain B: L.2, Q.6, G.26, T.27, G.28, K.29, S.30, I.31, F.181, R.182, T.476 Ligands: ALF.7, MG.8 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:S.3, B:Q.6, B:Q.6, B:G.26, B:T.27, B:T.27, B:G.28, B:K.29, B:S.30, B:I.31, B:T.476 Salt bridges: B:K.29, B:R.182, B:R.182 pi-Stacking: B:F.181, B:F.181

2 x ALF: TETRAFLUOROALUMINATE ION(Non-covalent)

ALF.4: 10 residues within 4Å: Chain A: A.25, G.26, K.29, E.107, Q.146, R.182, G.474, R.499 Ligands: ADP.3, MG.5 No protein-ligand interaction detected (PLIP) ALF.7: 11 residues within 4Å: Chain B: A.25, G.26, K.29, S.30, E.107, Q.146, R.182, G.474, R.499 Ligands: ADP.6, MG.8 No protein-ligand interaction detected (PLIP)

2 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 4 residues within 4Å: Chain A: S.30, E.107 Ligands: ADP.3, ALF.4 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:S.30, H2O.3, H2O.3, H2O.5 MG.8: 4 residues within 4Å: Chain B: S.30, E.107 Ligands: ADP.6, ALF.7 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:S.30, H2O.15, H2O.17

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.9: 2 residues within 4Å: Chain B: G.45, R.46 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.46 Salt bridges: B:R.46

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lu, K.Y. et al., Insights into the structural and mechanistic basis of multifunctional S. cerevisiae Pif1p helicase. Nucleic Acids Res. (2018)

Release Date

2017-12-13

Peptides

ATP-dependent DNA helicase PIF1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

ATP-dependent DNA helicase PIF1

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