6SF8 | pdb_00006sf8

Trypanosoma cruzi farnesyl diphosphate synthase in complex with fragment j51

PDB DOI: https://doi.org/10.2210/pdb6SF8/pdb

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

Deposited: 2019-08-01 Released: 2020-08-26
Deposition Author(s): Magari, F., Heine, A., Klebe, G.
Funding Organization(s): European Union

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.62 Å
R-Value Free:
0.192 (Depositor), 0.200 (DCC)
R-Value Work:
0.173 (Depositor), 0.180 (DCC)
R-Value Observed:
0.174 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Trypanosoma cruzi farnesyl diphosphate synthase in complex with fragment j51

Magari, F., Heine, A., Klebe, G.

To be published.

Macromolecule Content

Total Structure Weight: 41.55 kDa
Atom Count: 3,169
Modeled Residue Count: 361
Deposited Residue Count: 362
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Farnesyl diphosphate synthase	A	362	Trypanosoma cruzi	Mutation(s): 0
UniProt
Find proteins for Q8WS26 (Trypanosoma cruzi) Explore Q8WS26 Go to UniProtKB: Q8WS26
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8WS26
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
47Y (Subject of Investigation/LOI) Query on 47Y 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]	3-[(4E)-4-imino-5,6-dimethylfuro[2,3-d]pyrimidin-3(4H)-yl]-N,N-dimethylpropan-1-amine C₁₃ H₂₀ N₄ O BVYQUDYGRJSOAT-WYMLVPIESA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
SO4 Query on SO4 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]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.62 Å
R-Value Free: 0.192 (Depositor), 0.200 (DCC)
R-Value Work: 0.173 (Depositor), 0.180 (DCC)
R-Value Observed: 0.174 (Depositor)

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.903	α = 90
b = 57.903	β = 90
c = 398.288	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2020-08-26

Deposition Author(s):

Funding Organization	Location	Grant Number
European Union		--

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

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.