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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free:
0.192 (Depositor), 0.193 (DCC)
R-Value Work:
0.160 (Depositor), 0.161 (DCC)
R-Value Observed:
0.161 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Literature

TbrPDEB1-inhibitor complex

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

To be published.

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

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| 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8WQX9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PIL Query on PIL Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain E [auth A] MOL2 format, chain J [auth B] MOL2 format, chain E [auth A] mmCIF format, chain J [auth B] mmCIF format, chain E [auth A]	E [auth A], J [auth B]	3-(CYCLOPENTYLOXY)-N-(3,5-DICHLOROPYRIDIN-4-YL)-4-METHOXYBENZAMIDE C₁₈ H₁₈ Cl₂ N₂ O₃ RRRUXBQSQLKHEL-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain J [auth B] Interactions & Density Focus chain E [auth A] Focus chain J [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain C [auth A] MOL2 format, chain H [auth B] MOL2 format, chain C [auth A] mmCIF format, chain H [auth B] mmCIF format, chain C [auth A]	C [auth A], H [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain H [auth B] Interactions & Density Focus chain C [auth A] Focus chain H [auth B]
GAI Query on GAI Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	GUANIDINE C H₅ N₃ ZRALSGWEFCBTJO-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
EOH Query on EOH Download:Ideal Coordinates CCD File SDF format, chain K [auth B] MOL2 format, chain K [auth B] mmCIF format, chain K [auth B]	K [auth B]	ETHANOL C₂ H₆ O LFQSCWFLJHTTHZ-UHFFFAOYSA-N		Interactions Focus chain K [auth B] Interactions & Density Focus chain K [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain D [auth A] MOL2 format, chain I [auth B] MOL2 format, chain D [auth A] mmCIF format, chain I [auth B] mmCIF format, chain D [auth A]	D [auth A], I [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain I [auth B] Interactions & Density Focus chain D [auth A] Focus chain I [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.192 (Depositor), 0.193 (DCC)
R-Value Work: 0.160 (Depositor), 0.161 (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

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2015-05-20

Deposition Author(s):

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 (Full details and data files)

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