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), 0.273 (DCC)
R-Value Work:
0.224 (Depositor), 0.247 (DCC)
R-Value Observed:
0.225 (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 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:

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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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), 0.273 (DCC)
R-Value Work: 0.224 (Depositor), 0.247 (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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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

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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.