8R6N

Crystal structure of Candida glabrata Bdf1 bromodomain 2 bound to a pyridoindole ligand

PDB DOI: https://doi.org/10.2210/pdb8R6N/pdb

Classification: TRANSCRIPTION
Organism(s): Nakaseomyces glabratus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2023-11-22 Released: 2024-10-30
Deposition Author(s): Petosa, C., Wei, K., McKenna, C.E., Govin, J.
Funding Organization(s): Agence Nationale de la Recherche (ANR)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.11 Å
R-Value Free: 0.287
R-Value Work: 0.257
R-Value Observed: 0.259

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Humanized Candida and NanoBiT Assays Expedite Discovery of Bdf1 Bromodomain Inhibitors with Antifungal Potential against invasive Candida infection

Wei, K., Arlotto, M., Overhulse, J.M., Dinh, T.A., Zhou, Y., Dupper, N.J., Yang, J., Kashemirov, B.A., Dawi, H., Garnaud, C., Bourgine, G., Mietton, F., Champleboux, M., Larabi, A., Hayat, Y., Indorato, R.L., Noirclerc-Savoye, M., Skoufias, D., Cornet, M., Rabut, G., McKenna, C.E., Petosa, C., Govin, J.

(2024) Advanced Science

Macromolecule Content

Total Structure Weight: 14.19 kDa
Atom Count: 1,004
Modelled Residue Count: 116
Deposited Residue Count: 118
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Candida glabrata strain CBS138 chromosome C complete sequence	A	118	Nakaseomyces glabratus	Mutation(s): 0 Gene Names: CAGL0C02541g
UniProt
Find proteins for Q6FWV7 (Candida glabrata (strain ATCC 2001 / BCRC 20586 / JCM 3761 / NBRC 0622 / NRRL Y-65 / CBS 138)) Explore Q6FWV7 Go to UniProtKB: Q6FWV7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q6FWV7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
Y7B (Subject of Investigation/LOI) Query on Y7B Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	2-ethanoyl-~{N}-(4-morpholin-4-ylphenyl)-1,3,4,5-tetrahydropyrido[4,3-b]indole-8-carboxamide C₂₄ H₂₆ N₄ O₃ SWCZIQFQNPAUEC-UHFFFAOYSA-N		Interactions Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.11 Å
R-Value Free: 0.287
R-Value Work: 0.257
R-Value Observed: 0.259
Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.582	α = 90
b = 67.582	β = 90
c = 152.83	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
AutoProcess	data reduction
STARANISO	data scaling
MOLREP	phasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Released Date: 2024-10-30

Deposition Author(s):

Funding Organization	Location	Grant Number
Agence Nationale de la Recherche (ANR)	France	--

Revision History (Full details and data files)

Version 1.0: 2024-10-30
Type: Initial release

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.