6AN4 | pdb_00006an4

Crystal structure of Escherichia coli HPPK in complex with bisubstrate analogue inhibitor HP-39 (J1F)

• PDB DOI: https://doi.org/10.2210/pdb6AN4/pdb

• Classification: TRANSFERASE/INHIBITOR
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-08-12 Released: 2018-08-15 
• Deposition Author(s): Shaw, G.X., Shi, G., Ji, X.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.47 Å
• R-Value Free: 
  0.210 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.200 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.200 (Depositor) 

Literature

Bisubstrate analog inhibitors of HPPK: Transition state mimetics

Shaw, X.G., Shi, G., 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: 1,606 
• Modeled Residue Count: 151 
• Deposited Residue Count: 158 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase	A	158	Escherichia coli K-12	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
J1F	B [auth A]	((2-(2-amino-7,7-dimethyl-4-oxo-3,4,7,8-tetrahydropteridine-6-carboxamido)-N-(2-((((2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl)methyl)amino)-2-oxoethyl)acetamido)methyl)phosphonic acid C24 H32 N13 O10 P IHZBIHWJVSGIOO-MDNHXVGFSA-N
CL	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.47 Å
• R-Value Free:  0.210 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.200 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.200 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.778	α = 90
b = 48.092	β = 90
c = 77.043	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data processing
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-08-15 
Deposition Author(s): Shaw, G.X., Shi, G., Ji, X.

Revision History  

• Version 1.0: 2018-08-15
  Type: Initial release
  
• Version 1.1: 2023-08-30
  Changes: Data collection, Database references, Structure summary