4PHL | pdb_00004phl

TbrPDEB1-inhibitor complex

• PDB DOI: https://doi.org/10.2210/pdb4PHL/pdb

• Classification: Hydrolase/Hydrolase Inhibitor
• Organism(s): Trypanosoma brucei
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-05-06 Released: 2015-05-20 
• Deposition Author(s): Choy, M.S., Bland, N., Peti, W., Page, R.
• Funding Organization(s): National Science Foundation (NSF, United States), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.192 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.160 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.161 (Depositor) 

Starting Model: experimental

Literature

TbrPDEB1-inhibitor complex

Bland, N., Choy, M.S., Pollastri, M., Campbell, R., Peti, W., Page, R.

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: 79.33 kDa 
• Atom Count: 5,753 
• Modeled Residue Count: 662 
• Deposited Residue Count: 694 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Class 1 phosphodiesterase PDEB1	A, B	347	Trypanosoma brucei	Mutation(s): 0  Gene Names: PDEB1 EC: 3.1.4
UniProt
Find proteins for Q8WQX9 (Trypanosoma brucei) Explore Q8WQX9  Go to UniProtKB:  Q8WQX9

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PIL	E [auth A], J [auth B]	3-(CYCLOPENTYLOXY)-N-(3,5-DICHLOROPYRIDIN-4-YL)-4-METHOXYBENZAMIDE C18 H18 Cl2 N2 O3 RRRUXBQSQLKHEL-UHFFFAOYSA-N
GOL	G [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	C [auth A], H [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
GAI	F [auth A]	GUANIDINE C H5 N3 ZRALSGWEFCBTJO-UHFFFAOYSA-N
EOH	K [auth B]	ETHANOL C2 H6 O LFQSCWFLJHTTHZ-UHFFFAOYSA-N
MG	D [auth A], I [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.192 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.160 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.161 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110.195	α = 90
b = 119.265	β = 106.97
c = 68.144	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	phasing
HKL-3000	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2015-05-20 
Deposition Author(s): Choy, M.S., Bland, N., Peti, W., Page, R.

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Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	--
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	--

Revision History  

• Version 1.0: 2015-05-20
  Type: Initial release
  
• Version 1.1: 2017-09-06
  Changes: Author supporting evidence, Database references, Derived calculations, Other, Source and taxonomy
• Version 1.2: 2017-11-22
  Changes: Refinement description
• Version 1.3: 2019-11-27
  Changes: Author supporting evidence
• Version 1.4: 2022-03-23
  Changes: Author supporting evidence, Database references, Derived calculations, Refinement description
• Version 1.5: 2023-09-27
  Changes: Data collection, Refinement description