9FB8

XChem refined PIF1-x0076 complex

• PDB DOI: https://doi.org/10.2210/pdb9FB8/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-05-12 Released: 2024-09-18 
• Deposition Author(s): Bax, B.D., Antson, A.A., Sanders, C.M., Brandao-Neto, J.
• Funding Organization(s): Diamond Light Source

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.73 Å
• R-Value Free: 0.211 
• R-Value Work: 0.173 

Starting Model: experimental

Literature

Structure-based discovery of first on-target inhibitors of the human PIF1 helicase

Sanders, C.M., Bax, B.D.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 46.65 kDa 
• Atom Count: 3,675 
• Modelled Residue Count: 418 
• Deposited Residue Count: 419 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP-dependent DNA helicase PIF1	A	419	Homo sapiens	Mutation(s): 0  Gene Names: PIF1, C15orf20 EC: 3.6.4.12
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H611 (Homo sapiens) Explore Q9H611  Go to UniProtKB:  Q9H611
PHAROS:  Q9H611 GTEx:  ENSG00000140451

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ANP	B [auth A]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C10 H17 N6 O12 P3 PVKSNHVPLWYQGJ-KQYNXXCUSA-N
O0J (Subject of Investigation/LOI)	D [auth A], E [auth A]	N-[4-(2-amino-1,3-thiazol-4-yl)phenyl]acetamide C11 H11 N3 O S VBBNSESFUHRMJU-UHFFFAOYSA-N
DMS	F [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
MG	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.73 Å
• R-Value Free: 0.211 
• R-Value Work: 0.173 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.6	α = 90
b = 143.714	β = 90
c = 77.238	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
DIALS	data scaling
REFMAC	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-09-18 
Deposition Author(s): Bax, B.D., Antson, A.A., Sanders, C.M., Brandao-Neto, J.

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Funding Organization	Location	Grant Number
Diamond Light Source	United Kingdom	LB19204

Revision History  

• Version 1.0: 2024-09-18
  Type: Initial release