5VS7

Bromodomain of PF3D7_1475600 from Plasmodium falciparum complexed with peptide H4K5ac

• PDB DOI: https://doi.org/10.2210/pdb5VS7/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Plasmodium falciparum 3D7, Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-05-11 Released: 2017-05-31 
• Deposition Author(s): Hou, C.F.D., Loppnau, P., Dong, A., Bountra, C., Edwards, A.M., Arrowsmith, C.H., Hui, R., Walker, J.R., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.04 Å
• R-Value Free: 0.244 
• R-Value Work: 0.210 
• R-Value Observed: 0.212 

Starting Model: experimental

Literature

Bromodomain of PF3D7_1475600 from Plasmodium falciparum complexed with peptide H4K5ac

Hou, C.F.D., Loppnau, P., Dong, A., Bountra, C., Edwards, A.M., Arrowsmith, C.H., Hui, R., Walker, J.R., Structural Genomics Consortium (SGC)

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: isothermal titration calorimetry

Macromolecule Content

• Total Structure Weight: 15.21 kDa 
• Atom Count: 1,094 
• Modelled Residue Count: 124 
• Deposited Residue Count: 126 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bromodomain protein, putative	A	119	Plasmodium falciparum 3D7	Mutation(s): 0  Gene Names: PF14_0724, PF3D7_1475600
UniProt
Find proteins for Q8IK82 (Plasmodium falciparum (isolate 3D7)) Explore Q8IK82  Go to UniProtKB:  Q8IK82

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
H4K5ac peptide	B [auth P]	7	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	C [auth A], D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
ALY	B [auth P]	L-PEPTIDE LINKING	C8 H16 N2 O3		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.04 Å
• R-Value Free: 0.244 
• R-Value Work: 0.210 
• R-Value Observed: 0.212 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.11	α = 90
b = 41.51	β = 90
c = 73.09	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
HKL-2000	data collection
HKL-2000	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-05-31 
Deposition Author(s): Hou, C.F.D., Loppnau, P., Dong, A., Bountra, C., Edwards, A.M., Arrowsmith, C.H., Hui, R., Walker, J.R., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2017-05-31
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Refinement description
• Version 1.2: 2018-01-24
  Changes: Database references, Structure summary
• Version 1.3: 2023-10-04
  Changes: Data collection, Database references, Refinement description
• Version 1.4: 2023-11-15
  Changes: Data collection
• Version 1.5: 2024-11-20
  Changes: Structure summary