6SII | pdb_00006sii

T. brucei FPPS in complex with 1-((1H-indol-3-yl)methyl)-N-(3-chlorobenzyl)piperidin-4-amine

PDB DOI: https://doi.org/10.2210/pdb6SII/pdb

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

Deposited: 2019-08-09 Released: 2020-08-26
Deposition Author(s): Muenzker, L., Petrick, J.K., Schleberger, C., Jahnke, W.
Funding Organization(s): Other government, Marie Sklodowska-Curie Actions, FragNET ITN

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.33 Å
R-Value Free:
0.276 (Depositor), 0.303 (DCC)
R-Value Work:
0.250 (Depositor), 0.271 (DCC)
R-Value Observed:
0.252 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

T. brucei FPPS

Muenzker, L., Jahnke, W.

To be published.

Macromolecule Content

Total Structure Weight: 42.62 kDa
Atom Count: 2,650
Modeled Residue Count: 328
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
LEZ (Subject of Investigation/LOI) Query on LEZ 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]	~{N}-[(3-chlorophenyl)methyl]-1-(1~{H}-indol-3-ylmethyl)piperidin-4-amine C₂₁ H₂₄ Cl N₃ ZBFRXMWMJAMISF-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
GOL Query on GOL 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]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-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: 0.276 (Depositor), 0.303 (DCC)
R-Value Work: 0.250 (Depositor), 0.271 (DCC)
R-Value Observed: 0.252 (Depositor)

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.631	α = 90
b = 61.631	β = 90
c = 342.247	γ = 120

Software Package:

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

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
Other government	Switzerland	675899
Marie Sklodowska-Curie Actions, FragNET ITN		--

Revision History (Full details and data files)

Version 1.0: 2020-08-26
Type: Initial release
Version 1.1: 2024-01-24
Changes: Data collection, Database references, Refinement description

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