6R39 | pdb_00006r39

T. brucei FPPS in complex with 1-(carboxymethyl)-1H-benzo[g]indole-2-carboxylic acid

PDB DOI: https://doi.org/10.2210/pdb6R39/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: 2.60 Å
R-Value Free:
0.257 (Depositor), 0.330 (DCC)
R-Value Work:
0.234 (Depositor), 0.270 (DCC)
R-Value Observed:
0.235 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 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: 42.44 kDa
Atom Count: 2,634
Modeled Residue Count: 327
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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BFH Query on BFH 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]	1-(carboxymethyl)-1H-benzo[g]indole-2-carboxylic acid C₁₅ H₁₁ N O₄ AKGLRHRNGGDMDM-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.257 (Depositor), 0.330 (DCC)
R-Value Work: 0.234 (Depositor), 0.270 (DCC)
R-Value Observed: 0.235 (Depositor)

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.336	α = 90
b = 61.336	β = 90
c = 340.077	γ = 120

Software Package:

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

Structure Validation

View Full Validation Report

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: 2023-03-01
Changes: Database references
Version 1.3: 2024-02-07
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.