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232,829 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Source Organism Taxonomy Name (Full Lineage) = "Saccharomyces cerevisiae YJM789"

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Search Summary

This query matches 523 Structures.

Refinements

Structure Determination Methodology

	computational (453)
	experimental (70)

CSM Source Database

	AlphaFoldDB (414)
	ModelArchive (39)

pLDDT Global Quality Score

	< 50.0 (10)
	50.0 - 70.0 (127)
	70.0 - 90.0 (260)
	> 90.0 (56)

Scientific Name of Source Organism

	Saccharomyces cerevisiae YJM789 (484)
	Saccharomyces cerevisiae S288C (41)
	Saccharomyces cerevisiae (strain YJM789) (39)
	Saccharomyces cerevisiae (4)
	Homo sapiens (2)
	Escherichia coli K-12 (1)
	Human coronavirus OC43 (1)
	Murine hepatitis virus (1)
	Saccharomyces cerevisiae (strain Lalvin EC1118 / Prise de mousse) (1)
	Saccharomyces cerevisiae (strain RM11-1a) (1)

More...

Taxonomy

	Eukaryota (520)
	Eukaryota (eukaryotes) (39)
	Riboviria (3)
	Bacteria (1)
	other sequences (1)

Experimental Method

	X-RAY DIFFRACTION (67)
	SOLUTION NMR (2)
	ELECTRON MICROSCOPY (1)

Polymer Entity Type

	Protein (523)
	DNA (2)
	RNA (1)

Refinement Resolution (Å)

	1.0 - 1.5 (6)
	1.5 - 2.0 (15)
	2.0 - 2.5 (32)
	2.5 - 3.0 (10)
	3.0 - 3.5 (3)
	3.5 - 4.0 (1)
	4.0 - 4.5 (1)

Release Date

	2005 - 2009 (11)
	2010 - 2014 (4)
	2015 - 2019 (38)
	2020 - 2024 (469)
	2025 - 2029 (1)

Enzyme Classification Name

	Hydrolases (62)
	Oxidoreductases (57)
	Transferases (36)
	Ligases (6)
	Isomerases (6)
	Lyases (4)

Membrane Protein Annotation

	PDBTM (35)
	MemProtMD (33)
	OPM (4)

Symmetry Type

	Asymmetric (514)
	Cyclic (9)
	Dihedral (1)
	Helical (1)

SCOP Classification

	All alpha proteins (11)
	Artifacts (3)
	Alpha and beta proteins (a/b) (2)
	Membrane and cell surface proteins and peptides (2)

AllSelected

1 to 25 of 523 Structures

Page 1 of 21

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2RBT	Download File View File

n-methylbenzylamine in complex with Cytochrome C Peroxidase W191G

Graves, A.P., Boyce, S.E., Shoichet, B.K.

(2008) J Mol Biology 377: 914-934

Released	2008-04-01
Method	X-RAY DIFFRACTION 1.24 Å
Organisms	Saccharomyces cerevisiae YJM789
Macromolecule	Cytochrome C Peroxidase (protein)
Unique Ligands	271, HEM, MPD, PO4

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2RBU	Download File View File

Cytochrome C Peroxidase in complex with cyclopentane-carboximidamide

Graves, A.P., Boyce, S.E., Shoichet, B.K.

(2008) J Mol Biology 377: 914-934

Released	2008-03-18
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Saccharomyces cerevisiae YJM789
Macromolecule	Cytochrome C Peroxidase (protein)
Unique Ligands	273, HEM

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2RBV	Download File View File

Cytochrome C Peroxidase in complex with (1-methyl-1h-pyrrol-2-yl)-methylamine

Graves, A.P., Boyce, S.E., Shoichet, B.K.

(2008) J Mol Biology 377: 914-934

Released	2008-03-18
Method	X-RAY DIFFRACTION 1.39 Å
Organisms	Saccharomyces cerevisiae YJM789
Macromolecule	Cytochrome C Peroxidase (protein)
Unique Ligands	278, HEM, PO4

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2RBW	Download File View File

Cytochrome C Peroxidase W191G in complex with 1,2-dimethyl-1h-pyridin-5-amine

Graves, A.P., Boyce, S.E., Shoichet, B.K.

(2008) J Mol Biology 377: 914-934

Released	2008-03-18
Method	X-RAY DIFFRACTION 1.5 Å
Organisms	Saccharomyces cerevisiae YJM789
Macromolecule	Cytochrome C Peroxidase (protein)
Unique Ligands	275, HEM, PO4

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2RBX	Download File View File

Cytochrome C Peroxidase W191G in complex with pyrimidine-2,4,6-triamine.

Graves, A.P., Boyce, S.E., Shoichet, B.K.

(2008) J Mol Biology 377: 914-934

Released	2008-04-01
Method	X-RAY DIFFRACTION 1.5 Å
Organisms	Saccharomyces cerevisiae YJM789
Macromolecule	Cytochrome C Peroxidase (protein)
Unique Ligands	3AY, HEM, PO4

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2RBY	Download File View File

1-methyl-5-imidazolecarboxaldehyde in complex with Cytochrome C Peroxidase W191G

Graves, A.P., Boyce, S.E., Shoichet, B.K.

(2008) J Mol Biology 377: 914-934

Released	2008-03-18
Method	X-RAY DIFFRACTION 1.5 Å
Organisms	Saccharomyces cerevisiae YJM789
Macromolecule	Cytochrome C Peroxidase (protein)
Unique Ligands	280, HEM, PO4

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2RBZ	Download File View File

Cytochrome C Peroxidase W191G in complex 3-methoxypyridine

Graves, A.P., Boyce, S.E., Shoichet, B.K.

(2008) J Mol Biology 377: 914-934

Released	2008-03-18
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Saccharomyces cerevisiae YJM789
Macromolecule	Cytochrome C Peroxidase (protein)
Unique Ligands	282, HEM, PO4

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2RC0	Download File View File

Cytochrome C Peroxidase W191G in complex with 2-imino-4-methylpiperdine

Graves, A.P., Boyce, S.E., Shoichet, B.K.

(2008) J Mol Biology 377: 914-934

Released	2008-03-18
Method	X-RAY DIFFRACTION 1.5 Å
Organisms	Saccharomyces cerevisiae YJM789
Macromolecule	Cytochrome C Peroxidase (protein)
Unique Ligands	284, HEM, PO4

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2RC1	Download File View File

Cytochrome C Peroxidase W191G in complex with 2,4,5-trimethyl-3-oxazoline

Graves, A.P., Boyce, S.E., Shoichet, B.K.

(2008) J Mol Biology 377: 914-934

Released	2008-04-01
Method	X-RAY DIFFRACTION 2.49 Å
Organisms	Saccharomyces cerevisiae YJM789
Macromolecule	Cytochrome C Peroxidase (protein)
Unique Ligands	285, HEM

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2RC2	Download File View File

Cytochrome C Peroxidase W191G in complex with 1-methyl-2-vinyl-pyridinium

Graves, A.P., Boyce, S.E., Shoichet, B.K.

(2008) J Mol Biology 377: 914-934

Released	2008-03-18
Method	X-RAY DIFFRACTION 1.5 Å
Organisms	Saccharomyces cerevisiae YJM789
Macromolecule	Cytochrome C Peroxidase (protein)
Unique Ligands	286, HEM

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3E2V	Download File View File

Crystal structure of an uncharacterized amidohydrolase from Saccharomyces cerevisiae

Bonanno, J.B., Dickey, M., Bain, K.T., Hu, S., Romero, R., Smith, D., Wasserman, S., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

To be published

Released	2008-08-26
Method	X-RAY DIFFRACTION 1.5 Å
Organisms	Saccharomyces cerevisiae YJM789
Macromolecule	3'-5'-exonuclease (protein)
Unique Ligands	GOL, MG

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3MKQ	Download File View File

Crystal structure of yeast alpha/betaprime-COP subcomplex of the COPI vesicular coat

Lee, C., Goldberg, J.

(2010) Cell 142: 123-132

Released	2010-07-14
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Saccharomyces cerevisiae Saccharomyces cerevisiae YJM789
Macromolecule	Coatomer beta'-subunit (protein) Coatomer subunit alpha (protein)

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4G1B	Download File View File

X-ray structure of yeast flavohemoglobin in complex with econazole

El Hammi, E., Warkentin, E., Demmer, U., Baciou, L., Ermler, U.

(2012) FEBS J 279: 4565-4575

Released	2012-11-14
Method	X-RAY DIFFRACTION 3 Å
Organisms	Saccharomyces cerevisiae YJM789
Macromolecule	Flavohemoglobin (protein)
Unique Ligands	ECN, FAD, HEM

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4G1V	Download File View File

X-ray structure of yeast flavohemoglobin

El Hammi, E., Warkentin, E., Demmer, U., Baciou, L., Ermler, U.

(2012) FEBS J 279: 4565-4575

Released	2012-11-14
Method	X-RAY DIFFRACTION 2.098 Å
Organisms	Saccharomyces cerevisiae YJM789
Macromolecule	Flavohemoglobin (protein)
Unique Ligands	FAD, HEM, K, NO2

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4U1E	Download File View File

Crystal structure of the eIF3b-CTD/eIF3i/eIF3g-NTD translation initiation complex

Zhang, S., Erzberger, J.P., Schaefer, T., Ban, N.

(2014) Cell 158: 1123-1135

Released	2014-09-10
Method	X-RAY DIFFRACTION 2 Å
Organisms	Saccharomyces cerevisiae S288C Saccharomyces cerevisiae YJM789
Macromolecule	Eukaryotic translation initiation factor 3 subunit B (protein) Eukaryotic translation initiation factor 3 subunit G (protein) Eukaryotic translation initiation factor 3 subunit I (protein)

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4WA6	Download File View File

Structure of yeast SAGA DUBm with Sgf73 N59D mutant at 2.36 angstroms resolution

Wolberger, C., Yan, M.

To be published

Released	2015-03-04
Method	X-RAY DIFFRACTION 2.36 Å
Organisms	Saccharomyces cerevisiae S288C Saccharomyces cerevisiae YJM789
Macromolecule	SAGA-associated factor 11 (protein) SAGA-associated factor 73 (protein) Transcription and mRNA export factor SUS1 (protein) Ubiquitin carboxyl-terminal hydrolase 8 (protein)
Unique Ligands	ZN

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4WMZ	Download File View File

S. cerevisiae CYP51 complexed with fluconazole in the active site

Sagatova, A., Keniya, M.V., Wilson, R., Wilbanks, S.M., Monk, B.C., Tyndall, J.D.A.

(2015) Antimicrob Agents Chemother 59: 4982-4989

Released	2015-07-01
Method	X-RAY DIFFRACTION 2.05 Å
Organisms	Saccharomyces cerevisiae YJM789
Macromolecule	Lanosterol 14-alpha demethylase (protein)
Unique Ligands	HEM, TPF

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4ZDY	Download File View File

Saccharomyces cerevisiae CYP51 (Lanosterol 14-alpha demethylase) Y140F mutant complexed with itraconazole

Sagatova, A., Keniya, M.V., Wilson, R.K., Tyndall, J.D.A., Monk, B.C.

(2016) Sci Rep 6: 26213-26213

Released	2016-03-30
Method	X-RAY DIFFRACTION 2.02 Å
Organisms	Saccharomyces cerevisiae YJM789
Macromolecule	Lanosterol 14-alpha demethylase (protein)
Unique Ligands	1YN, HEM

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4ZDZ	Download File View File

Saccharomyces cerevisiae CYP51 (Lanosterol 14-alpha demethylase) Y140F mutant complexed with fluconazole

Sagatova, A., Keniya, M.V., Wilson, R.K., Tyndall, J.D.A., Monk, B.C.

(2016) Sci Rep 6: 26213-26213

Released	2016-03-30
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Saccharomyces cerevisiae YJM789
Macromolecule	Lanosterol 14-alpha demethylase (protein)
Unique Ligands	HEM, TPF

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4ZE0	Download File View File

Saccharomyces cerevisiae CYP51 (Lanosterol 14-alpha demethylase) Y140F mutant complexed with Voriconazole

Sagatova, A., Keniya, M.V., Wilson, R., Tyndall, J.D.A., Monk, B.C.

(2016) Sci Rep 6: 26213-26213

Released	2016-03-30
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Saccharomyces cerevisiae YJM789
Macromolecule	Lanosterol 14-alpha demethylase (protein)
Unique Ligands	HEM, VOR

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4ZE1	Download File View File

Saccharomyces cerevisiae CYP51 Y140F mutant complexed with posaconazole in the active site

Sagatova, A., Keniya, M.V., Wilson, R., Tyndall, J.D.A., Monk, B.C.

(2016) Sci Rep 6: 26213-26213

Released	2016-03-30
Method	X-RAY DIFFRACTION 2.05 Å
Organisms	Saccharomyces cerevisiae YJM789
Macromolecule	Lanosterol 14-alpha demethylase (protein)
Unique Ligands	HEM, X2N

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4ZE2	Download File View File

Saccharomyces cerevisiae CYP51 (Lanosterol 14-alpha demethylase) Y140H mutant complexed with itraconazole

Sagatova, A., Keniya, M.V., Wilson, R., Monk, B.C., Tyndall, J.D.A.

(2016) Sci Rep 6: 26213-26213

Released	2016-03-30
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Saccharomyces cerevisiae YJM789
Macromolecule	Lanosterol 14-alpha demethylase (protein)
Unique Ligands	1YN, HEM

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4ZE3	Download File View File

Saccharomyces cerevisiae CYP51 (Lanosterol 14-alpha demethylase) Y140H mutant complexed with fluconazole

Sagatova, A., Keniya, M.V., Wilson, R., Monk, B.C., Tyndall, J.D.A.

(2016) Sci Rep 6: 26213-26213

Released	2016-03-30
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Saccharomyces cerevisiae YJM789
Macromolecule	Lanosterol 14-alpha demethylase (protein)
Unique Ligands	HEM, TPF

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4ZUX	Download File View File

SAGA DUB module Ubp8/Sgf11/Sus1/Sgf73 bound to ubiqitinated nucleosome

Morgan, M., Wolberger, C.

(2016) Science 351: 725-728

Released	2016-02-24
Method	X-RAY DIFFRACTION 3.82 Å
Organisms	Homo sapiens Saccharomyces cerevisiae S288C Saccharomyces cerevisiae YJM789 Xenopus laevis synthetic construct
Macromolecule	Unique protein chains: 9 Unique nucleic acid chains: 2
Unique Ligands	ZN

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5EAB	Download File View File

Saccharomyces cerevisiae CYP51 complexed with the plant pathogen inhibitor S-tebuconazole

Tyndall, J.D.A., Sabherwal, M., Sagatova, A.A., Keniya, M.V., Wilson, R.K., Woods, M.V., Monk, B.C.

(2016) PLoS One 11: e0167485-e0167485

Released	2016-02-10
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Saccharomyces cerevisiae YJM789
Macromolecule	Lanosterol 14-alpha demethylase (protein)
Unique Ligands	HEM, TBX