6B18 | pdb_00006b18

Crystal structure of PPK3 Class III in complex with inhibitor

• PDB DOI: https://doi.org/10.2210/pdb6B18/pdb

• Classification: transferase/transferase inhibitor
• Organism(s): Cytophaga hutchinsonii ATCC 33406
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2017-09-17 Released: 2019-01-16 
• Deposition Author(s): Nocek, B., Ruszkowski, M., Berlicki, L., Joachimiak, A., Yakunin, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.241 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.191 (Depositor), 0.199 (DCC) 
• R-Value Observed: 
  0.193 (Depositor) 

Literature

Structural Insights into Substrate Selectivity and Activity of Bacterial Polyphosphate Kinases

Nocek, B., Khusnutdinova, A.N., Ruszkowski, M., Flick, R., Burda, M., Batyrova, K., Brown, G., Mucha, A., Joachimiak, A., Berlicki, L., Yakunin, A.F.

(2018) ACS Catal 8: 10746-10760

• DOI: https://doi.org/10.1021/acscatal.8b03151

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: 36.12 kDa 
• Atom Count: 2,665 
• Modeled Residue Count: 299 
• Deposited Residue Count: 308 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PPK3 Class III	A	308	Cytophaga hutchinsonii ATCC 33406	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
C8A (Subject of Investigation/LOI)	B [auth A]	{[(4-benzylphenyl)amino]methylene}bis(phosphonic acid) C14 H17 N O6 P2 UUWAWXLKQDUPIO-UHFFFAOYSA-N
PO4 (Subject of Investigation/LOI)	C [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL (Subject of Investigation/LOI)	D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.241 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.191 (Depositor), 0.199 (DCC) 
• R-Value Observed: 0.193 (Depositor) 

Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 111.475	α = 90
b = 111.475	β = 90
c = 175.733	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-01-16 
Deposition Author(s): Nocek, B., Ruszkowski, M., Berlicki, L., Joachimiak, A., Yakunin, A.

Revision History  

• Version 1.0: 2019-01-16
  Type: Initial release
  
• Version 1.1: 2020-07-29
  Changes: Database references
• Version 1.2: 2024-03-13
  Changes: Data collection, Database references