SMTL ID : 9fb8.1

XChem refined PIF1-x0076 complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.73 Å

Oligo State

monomer

Ligands

1 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER

ANP.1: 20 residues within 4Å: Chain A: M.3, Q.4, L.5, S.6, Q.9, S.27, A.28, G.29, T.30, G.31, K.32, S.33, Y.34, E.105, Q.144, W.178, R.179, G.357, R.382 Ligands: MG.2 23 PLIP interactions: 23 interactions with chain A Hydrogen bonds: A:S.6, A:Q.9, A:Q.9, A:G.29, A:T.30, A:G.31, A:K.32, A:K.32, A:K.32, A:S.33, A:Y.34, A:Q.144, A:Q.144, A:R.179, A:R.179, A:R.382, A:R.382 Water bridges: A:S.33, A:E.105, A:G.357 pi-Stacking: A:W.178, A:W.178, A:W.178

1 x MG: MAGNESIUM ION

MG.2: 3 residues within 4Å: Chain A: S.33, E.105 Ligands: ANP.1 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:S.33, H2O.2, H2O.7, H2O.7

2 x O0J: N-[4-(2-amino-1,3-thiazol-4-yl)phenyl]acetamide

O0J.3: 15 residues within 4Å: Chain A: G.55, V.56, V.230, N.234, D.262, A.263, Q.264, C.265, P.266, M.280, Q.345, L.346, A.349, M.350, K.354 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:V.56, A:P.266, A:K.354 Hydrogen bonds: A:N.234, A:A.349 Water bridges: A:S.351 O0J.4: 5 residues within 4Å: Chain A: F.159, Q.160, R.404, H.407, F.408 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.408 Hydrogen bonds: A:Q.160 Water bridges: A:F.408 pi-Stacking: A:F.159

1 x DMS: DIMETHYL SULFOXIDE

DMS.5: 3 residues within 4Å: Chain A: C.224, D.229, T.233 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.222 Salt bridges: A:D.229

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wever, M.J.A. et al., Structure-based discovery of first inhibitors targeting the helicase activity of human PIF1. Nucleic Acids Res. (2024)

Release Date

2024-09-18

Peptides

ATP-dependent DNA helicase PIF1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

ATP-dependent DNA helicase PIF1