6R38 | pdb_00006r38

T. brucei FPPS in complex with 2-(2,5-dichlorobenzo[b]thiophen-3-yl)acetic acid

PDB DOI: https://doi.org/10.2210/pdb6R38/pdb

Classification: TRANSFERASE
Organism(s): Trypanosoma brucei
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2019-03-19 Released: 2020-04-08
Deposition Author(s): Muenzker, L., Petrick, J.K., Schleberger, C., Jahnke, W.
Funding Organization(s): Marie Sklodowska-Curie Actions, FragNET ITN

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.33 Å
R-Value Free:
0.249 (Depositor), 0.270 (DCC)
R-Value Work:
0.224 (Depositor), 0.250 (DCC)
R-Value Observed:
0.225 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Targeting Trypanosoma brucei FPPS by Fragment-based drug discovery

Muenzker, L., Wolfgang, J.

(2019) Thesis

DOI: https://doi.org/10.17192/z2019.0500

Macromolecule Content

Total Structure Weight: 42.51 kDa
Atom Count: 2,663
Modeled Residue Count: 331
Deposited Residue Count: 369
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Farnesyl pyrophosphate synthase	A	369	Trypanosoma brucei	Mutation(s): 0
UniProt
Find proteins for Q86C09 (Trypanosoma brucei) Explore Q86C09 Go to UniProtKB: Q86C09
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q86C09
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
JQE Query on JQE 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]	2-[2,5-bis(chloranyl)-1-benzothiophen-3-yl]ethanoic acid C₁₀ H₆ Cl₂ O₂ S BCQFHYKPVHGTMB-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
DMS Query on DMS Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.33 Å
R-Value Free: 0.249 (Depositor), 0.270 (DCC)
R-Value Work: 0.224 (Depositor), 0.250 (DCC)
R-Value Observed: 0.225 (Depositor)

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.839	α = 90
b = 60.839	β = 90
c = 339.99	γ = 120

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2020-04-08

Deposition Author(s):

Schleberger, C.

Funding Organization	Location	Grant Number
Marie Sklodowska-Curie Actions, FragNET ITN	Switzerland	675899

Revision History (Full details and data files)

Version 1.0: 2020-04-08
Type: Initial release
Version 1.1: 2021-10-27
Changes: Database references
Version 1.2: 2024-01-24
Changes: Data collection, Refinement description

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.