3PEH

Crystal Structure of the N-terminal domain of an HSP90 from Plasmodium Falciparum, PFL1070c in the presence of a thienopyrimidine derivative

• PDB DOI: https://doi.org/10.2210/pdb3PEH/pdb

• Classification: CHAPERONE
• Organism(s): Plasmodium falciparum 3D7
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-10-26 Released: 2010-11-17 
• Deposition Author(s): Wernimont, A.K., Tempel, W., Hutchinson, A., Weadge, J., Cossar, D., MacKenzie, F., Vedadi, M., Senisterra, G., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Weigelt, J., Wyatt, P.G., Fairlamb, A.H., MacKenzie, C., Ferguson, M.A.J., Hui, R., Pizarro, J.C., Hills, T., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free: 0.263 
• R-Value Work: 0.222 
• R-Value Observed: 0.224 

Starting Model: experimental

Literature

Crystal Structure of the N-terminal domain of an HSP90 from Plasmodium Falciparum, PFL1070c in the presence of a thienopyrimidine derivative

Wernimont, A.K., Tempel, W., Hutchinson, A., Weadge, J., Cossar, D., MacKenzie, F., Vedadi, M., Senisterra, G., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Weigelt, J., Wyatt, P.G., Fairlamb, A.H., MacKenzie, C., Ferguson, M.A.J., Hui, R., Pizarro, J.C., Hills, T.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 65.29 kDa 
• Atom Count: 4,012 
• Modelled Residue Count: 523 
• Deposited Residue Count: 562 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endoplasmin homolog	A, B	281	Plasmodium falciparum 3D7	Mutation(s): 0  Gene Names: PFL1070c
UniProt
Find proteins for Q8I0V4 (Plasmodium falciparum (isolate 3D7)) Explore Q8I0V4  Go to UniProtKB:  Q8I0V4

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IBD	C [auth A], E [auth B]	2-amino-4-{2,4-dichloro-5-[2-(diethylamino)ethoxy]phenyl}-N-ethylthieno[2,3-d]pyrimidine-6-carboxamide C21 H25 Cl2 N5 O2 S KQRDVNUCOWRFLN-UHFFFAOYSA-N
SO4	D [auth A], F [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free: 0.263 
• R-Value Work: 0.222 
• R-Value Observed: 0.224 
• Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.927	α = 90
b = 91.927	β = 90
c = 162.884	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data collection
DENZO	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-11-17 
Deposition Author(s): Wernimont, A.K., Tempel, W., Hutchinson, A., Weadge, J., Cossar, D., MacKenzie, F., Vedadi, M., Senisterra, G., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Weigelt, J., Wyatt, P.G., Fairlamb, A.H., MacKenzie, C., Ferguson, M.A.J., Hui, R., Pizarro, J.C., Hills, T., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2010-11-17
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-08
  Changes: Refinement description
• Version 1.3: 2019-07-17
  Changes: Data collection, Refinement description
• Version 1.4: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description