4PY6 | pdb_00004py6

Crystal Structure of bromodomain of PFA0510w from Plasmodium Falciparum

• PDB DOI: https://doi.org/10.2210/pdb4PY6/pdb

• Classification: PROTEIN BINDING
• Organism(s): Plasmodium falciparum 3D7
• Expression System: Cricetulus griseus
• Mutation(s): No 


• Deposited: 2014-03-26 Released: 2014-04-30 
• Deposition Author(s): Fonseca, M., Tallant, C., Hutchinson, A., Savitsky, P., Krojer, T., Filippakopoulos, P., Loppnau, P., Brennan, P.E., von Delft, F., Dong, A., Josling, G.A., Duffy, M.F., Arrowsmith, C.H., Bountra, C., Hui, R., Knapp, S., Wernimont, A.K., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.268 (Depositor), 0.289 (DCC) 
• R-Value Work: 
  0.237 (Depositor), 0.255 (DCC) 
• R-Value Observed: 
  0.239 (Depositor) 

Literature

Crystal Structure of bromodomain of PFA0510w from Plasmodium Falciparum

Fonseca, M., Tallant, C., Hutchinson, A., Savitsky, P., Krojer, T., Filippakopoulos, P., Loppnau, P., Brennan, P.E., von Delft, F., Dong, A., Josling, G.A., Duffy, M.F., Arrowsmith, C.H., Bountra, C., Hui, R., Knapp, S., Wernimont, A.K., Structural Genomics Consortium (SGC)

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 72.1 kDa 
• Atom Count: 4,733 
• Modeled Residue Count: 518 
• Deposited Residue Count: 580 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bromodomain protein, putative	A, B, C, D	145	Plasmodium falciparum 3D7	Mutation(s): 0  Gene Names: PFA0510w, PFA_0510w, PFUGPA_00085
UniProt
Find proteins for Q8I240 (Plasmodium falciparum (isolate 3D7)) Explore Q8I240  Go to UniProtKB:  Q8I240

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
R78	E [auth A], G [auth B], J [auth C], K [auth D]	4-{[(7R)-8-cyclopentyl-7-ethyl-5-methyl-6-oxo-5,6,7,8-tetrahydropteridin-2-yl]amino}-3-methoxy-N-(1-methylpiperidin-4-yl)benzamide C28 H39 N7 O3 XQVVPGYIWAGRNI-JOCHJYFZSA-N
EDO	F [auth A], H [auth B], I [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.268 (Depositor), 0.289 (DCC) 
• R-Value Work:  0.237 (Depositor), 0.255 (DCC) 
• R-Value Observed: 0.239 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.324	α = 90
b = 84.269	β = 90
c = 219.724	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
PHASER	phasing
BUSTER-TNT	refinement
PDB_EXTRACT	data extraction
XSCALE	data scaling
BUSTER	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-04-30 
Deposition Author(s): Fonseca, M., Tallant, C., Hutchinson, A., Savitsky, P., Krojer, T., Filippakopoulos, P., Loppnau, P., Brennan, P.E., von Delft, F., Dong, A., Josling, G.A., Duffy, M.F., Arrowsmith, C.H., Bountra, C., Hui, R., Knapp, S., Wernimont, A.K., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2014-04-30
  Type: Initial release
  
• Version 1.1: 2014-05-07
  Changes: Structure summary
• Version 1.2: 2024-02-28
  Changes: Data collection, Database references, Derived calculations