4QNS

Crystal structure of bromodomain from Plasmodium faciparum GCN5, PF3D7_0823300

PDB DOI: https://doi.org/10.2210/pdb4QNS/pdb

Classification: TRANSFERASE
Organism(s): Plasmodium falciparum 3D7
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2014-06-18 Released: 2014-07-16
Deposition Author(s): Fonseca, M., Tallant, C., Knapp, S., Loppnau, P., von Delft, F., Wernimont, A.K., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Hui, R., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.187
R-Value Work: 0.156
R-Value Observed: 0.158

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of bromodomain from Plasmodium faciparum GCN5, PF3D7_0823300

Fonseca, M., Tallant, C., Knapp, S., Loppnau, P., Hui, R., Wernimont, A.K., Arrowsmith, C.H., Edwards, A.M., Bountra, C.

To be published.

Macromolecule Content

Total Structure Weight: 51.87 kDa
Atom Count: 4,219
Modelled Residue Count: 415
Deposited Residue Count: 424
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone acetyltransferase GCN5, putative	A, B, C, D	106	Plasmodium falciparum 3D7	Mutation(s): 0 Gene Names: gcn5, PF08_0034, PFNF54_02299
UniProt
Find proteins for Q8IB67 (Plasmodium falciparum (isolate 3D7)) Explore Q8IB67 Go to UniProtKB: Q8IB67
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8IB67
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain O [auth B] SDF format, chain P [auth C] SDF format, chain Q [auth C] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth C] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain O [auth B] mmCIF format, chain P [auth C] mmCIF format, chain Q [auth C]	E [auth A] F [auth A] J [auth B] K [auth B] L [auth B] E [auth A], F [auth A], J [auth B], K [auth B], L [auth B], O [auth B], P [auth C], Q [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain O [auth B] Focus chain P [auth C] Focus chain Q [auth C] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain O [auth B] Focus chain P [auth C] Focus chain Q [auth C]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain M [auth B] SDF format, chain R [auth C] SDF format, chain S [auth D] SDF format, chain T [auth D] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain M [auth B] MOL2 format, chain R [auth C] MOL2 format, chain S [auth D] MOL2 format, chain T [auth D] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain M [auth B] mmCIF format, chain R [auth C] mmCIF format, chain S [auth D] mmCIF format, chain T [auth D]	G [auth A] H [auth A] I [auth A] M [auth B] R [auth C] G [auth A], H [auth A], I [auth A], M [auth B], R [auth C], S [auth D], T [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain M [auth B] Focus chain R [auth C] Focus chain S [auth D] Focus chain T [auth D] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain M [auth B] Focus chain R [auth C] Focus chain S [auth D] Focus chain T [auth D]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain N [auth B] SDF format, chain U [auth D] SDF format, chain V [auth D] MOL2 format, chain N [auth B] MOL2 format, chain U [auth D] MOL2 format, chain V [auth D] mmCIF format, chain N [auth B] mmCIF format, chain U [auth D] mmCIF format, chain V [auth D]	N [auth B], U [auth D], V [auth D]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain N [auth B] Focus chain U [auth D] Focus chain V [auth D] Interactions & Density Focus chain N [auth B] Focus chain U [auth D] Focus chain V [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.187
R-Value Work: 0.156
R-Value Observed: 0.158
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.217	α = 90
b = 98.871	β = 109.63
c = 50.439	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
XSCALE	data scaling

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2014-07-16

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2014-07-16
Type: Initial release
Version 1.1: 2018-01-31
Changes: Structure summary
Version 1.2: 2024-02-28
Changes: Data collection, Database references, Derived calculations