8SIF

Crystal structure of Escherichia coli HPPK in complex with bisubstrate inhibitor HP-101

• PDB DOI: https://doi.org/10.2210/pdb8SIF/pdb

• Classification: TRANSFERASE/INHIBITOR
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-04-16 Released: 2024-07-03 
• Deposition Author(s): Shaw, G.X., Shi, G., Ji, X.
• Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.235 
• R-Value Work: 0.178 
• R-Value Observed: 0.181 

Starting Model: experimental

Literature

The first bisubstrate inhibitor of HPPK exhibiting cell permeability

Shi, G., Shaw, G.X., Ji, X.

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)

Macromolecule Content

• Total Structure Weight: 18.7 kDa 
• Atom Count: 1,598 
• Modelled Residue Count: 158 
• Deposited Residue Count: 159 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase	A	159	Escherichia coli	Mutation(s): 0  Gene Names: folK, b0142, JW0138 EC: 2.7.6.3
UniProt
Find proteins for P26281 (Escherichia coli (strain K12)) Explore P26281  Go to UniProtKB:  P26281

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZX4 (Subject of Investigation/LOI)	B [auth A]	5'-S-{(2R,4R)-1-[3-(2-amino-4-oxo-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidin-5-yl)propyl]-2-carboxypiperidin-4-yl}-5'-thioadenosine C25 H32 N10 O6 S AOZGSZXCWJDLPF-LVEUASCASA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.235 
• R-Value Work: 0.178 
• R-Value Observed: 0.181 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.625	α = 90
b = 52.576	β = 102.58
c = 36.512	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
SCALEPACK	data scaling
DENZO	data reduction
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-07-03 
Deposition Author(s): Shaw, G.X., Shi, G., Ji, X.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	Intramural Research Program

Revision History  

• Version 1.0: 2024-07-03
  Type: Initial release