8R6K

Crystal structure of Candida glabrata Bdf1 bromodomain 1 bound to a phenyltriazine ligand

PDB DOI: https://doi.org/10.2210/pdb8R6K/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: 2.19 Å
R-Value Free: 0.247
R-Value Work: 0.209
R-Value Observed: 0.211

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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: 53.1 kDa
Atom Count: 4,102
Modelled Residue Count: 447
Deposited Residue Count: 456
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Candida glabrata strain CBS138 chromosome C complete sequence	A, B, C, D	114	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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
Y78 (Subject of Investigation/LOI) Query on Y78 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain I [auth B] SDF format, chain J [auth C] MOL2 format, chain E [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth C] mmCIF format, chain E [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth C]	E [auth A], I [auth B], J [auth C]	6-methyl-~{N}-[(5-methylfuran-2-yl)methyl]-3-(4-methylphenyl)-1,2,4-triazin-5-amine C₁₇ H₁₈ N₄ O FSPDKAUYNLMGSQ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain I [auth B] Focus chain J [auth C] Interactions & Density Focus chain E [auth A] Focus chain I [auth B] Focus chain J [auth C]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain K [auth C] SDF format, chain L [auth D] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain K [auth C] MOL2 format, chain L [auth D] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain K [auth C] mmCIF format, chain L [auth D]	F [auth A], G [auth A], K [auth C], L [auth D]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain K [auth C] Focus chain L [auth D] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain K [auth C] Focus chain L [auth D]
K Query on K Download Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]