6SI5 | pdb_00006si5

T. cruzi FPPS in complex with 1-methyl-5-(4,5,6,7-tetrahydrothieno[3,2-c]pyridine-5-carbonyl)pyridin-2(1H)-one

PDB DOI: https://doi.org/10.2210/pdb6SI5/pdb

Classification: TRANSFERASE
Organism(s): Trypanosoma cruzi
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2019-08-08 Released: 2020-08-26
Deposition Author(s): Petrick, J.K., Muenzker, L., Schleberger, C., Cornaciu, I., Clavel, D., Marquez, J.A., Jahnke, W.
Funding Organization(s): European Commission, Accelerated Early staGe drug dIScovery

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.260 (Depositor), 0.247 (DCC)
R-Value Work:
0.200 (Depositor), 0.194 (DCC)
R-Value Observed:
0.203 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Targeting farnesyl pyrophosphate synthase of Trypanosoma cruzi by fragment-based lead discovery

Petrick, J.K., Jahnke, W.

(2019) Thesis

DOI: https://doi.org/10.17192/z2019.0501

Macromolecule Content

Total Structure Weight: 41.83 kDa
Atom Count: 2,997
Modeled Residue Count: 354
Deposited Residue Count: 364
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Farnesyl diphosphate synthase	A	364	Trypanosoma cruzi	Mutation(s): 0
UniProt
Find proteins for Q8WS26 (Trypanosoma cruzi) Explore Q8WS26 Go to UniProtKB: Q8WS26
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8WS26
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
LEQ (Subject of Investigation/LOI) Query on LEQ Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	5-(6,7-dihydro-4~{H}-thieno[3,2-c]pyridin-5-ylcarbonyl)-1-methyl-pyridin-2-one C₁₄ H₁₄ N₂ O₂ S PXCRFQLKGNEWBG-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A]	C [auth A], D [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.260 (Depositor), 0.247 (DCC)
R-Value Work: 0.200 (Depositor), 0.194 (DCC)
R-Value Observed: 0.203 (Depositor)

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.061	α = 90
b = 58.061	β = 90
c = 396.793	γ = 120

Software Package:

Software Name	Purpose
BUSTER	refinement
Aimless	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2020-08-26

Deposition Author(s):

Schleberger, C.

Funding Organization	Location	Grant Number
European Commission		765555
Accelerated Early staGe drug dIScovery		765555

Revision History (Full details and data files)

Version 1.0: 2020-08-26
Type: Initial release
Version 1.1: 2023-03-01
Changes: Database references
Version 1.2: 2024-02-07
Changes: Data collection, Refinement description

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.