5VS7 | pdb_00005vs7

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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.04 Å
R-Value Free:
0.244 (Depositor), 0.259 (DCC)
R-Value Work:
0.210 (Depositor), 0.212 (DCC)
R-Value Observed:
0.212 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.5 of the entry. See complete history.

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.

Macromolecule Content

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

Macromolecules

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| 3D Structure

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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8IK82
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

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	3D Interactions
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
ALY Query on 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 (Depositor), 0.259 (DCC)
R-Value Work: 0.210 (Depositor), 0.212 (DCC)
R-Value Observed: 0.212 (Depositor)

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

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Entry History

Deposition Data

Released Date: 2017-05-31

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

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