6AN6 | pdb_00006an6

Crystal structure of Escherichia coli HPPK in complex with bisubstrate analogue inhibitor HP-72

• PDB DOI: https://doi.org/10.2210/pdb6AN6/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: 2.30 Å
• R-Value Free: 
  0.257 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.216 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.218 (Depositor) 

Starting Model: experimental

Literature

Bisubstrate analogue inhibitors of HPPK: Transition state mimetics

Shaw, G.X., Shi, G., Ji, X.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 37.3 kDa 
• Atom Count: 2,782 
• Modeled Residue Count: 316 
• Deposited Residue Count: 316 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase	A, B	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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
J1I	C [auth A], D [auth B]	5'-S-{2-[{2-[(2-amino-7,7-dimethyl-4-oxo-3,4,7,8-tetrahydropteridine-6-carbonyl)amino]ethyl}(phosphonomethyl)amino]ethyl}-5'-thioadenosine C24 H35 N12 O8 P S LNONYTMYGAJODO-HUYKWJOFSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.257 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.216 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.218 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.67	α = 90
b = 52.924	β = 103.42
c = 77.43	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
HKL-2000	data reduction
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
• Version 1.2: 2023-10-04
  Changes: Refinement description