5KNR

E. coli HPRT in complexed with 9-[(N-phosphonoethyl-N-phosphonoethoxyethyl)-2-aminoethyl]-guanine

• PDB DOI: https://doi.org/10.2210/pdb5KNR/pdb

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


• Deposited: 2016-06-28 Released: 2017-07-19 
• Deposition Author(s): Eng, W.S., Keough, D.T., Hockova, D., Janeba, Z.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.86 Å
• R-Value Free: 0.267 
• R-Value Work: 0.233 
• R-Value Observed: 0.236 

Starting Model: experimental

Literature

Crystal Structures of Acyclic Nucleoside Phosphonates in Complex with Escherichia coli Hypoxanthine Phosphoribosyltransferase

Eng, W.S., Hockova, D., Spacek, P., Baszczynski, O., Janeba, Z., Naesens, L., Keough, D.T., Guddat, L.W.

(2016) ChemistrySelect 1: 6267-6276

• DOI: https://doi.org/10.1002/slct.201601679

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 42.22 kDa 
• Atom Count: 2,785 
• Modelled Residue Count: 342 
• Deposited Residue Count: 364 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypoxanthine-guanine phosphoribosyltransferase	A, B	182	Escherichia coli	Mutation(s): 0  Gene Names: hpt, ACN002_0124 EC: 2.4.2.8
UniProt
Find proteins for P0A9M2 (Escherichia coli (strain K12)) Explore P0A9M2  Go to UniProtKB:  P0A9M2

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
3L5	C [auth A], E [auth B]	(2-{[2-(2-amino-6-oxo-3,6-dihydro-9H-purin-9-yl)ethyl][2-(2-phosphonoethoxy)ethyl]amino}ethyl)phosphonic acid C13 H24 N6 O8 P2 ONMAFLJUDYCSLA-UHFFFAOYSA-N
MG	D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.86 Å
• R-Value Free: 0.267 
• R-Value Work: 0.233 
• R-Value Observed: 0.236 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.617	α = 90
b = 84.617	β = 90
c = 167.116	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-07-19 
Deposition Author(s): Eng, W.S., Keough, D.T., Hockova, D., Janeba, Z.

Revision History  

• Version 1.0: 2017-07-19
  Type: Initial release
  
• Version 1.1: 2023-09-27
  Changes: Data collection, Database references, Refinement description