Protein Help

PDS5 / YMR076C Protein

Protein abundance data, domains, shared domains with other proteins, protein sequence retrieval for various strains, sequence-based physico-chemical properties, protein modification sites, and external identifiers for the protein.


Feature Type
ORF , Verified
Summary
Relocalizes to the cytosol in response to hypoxia

AlphaFold Protein Structure

AlphaFold, developed by DeepMind, is an AI program that accurately predicts protein structures from amino acid sequences, enabling visualization of protein conformations. The predicted structures can be accessed through the Protein Data Bank (PDB) and AlphaFold Protein Structure Database.


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Model Confidence

Very high
Confident
Low
Very low

Experimental Data

Contains experimentally-derived protein half-life data obtained using stable isotope labeling by amino acids (SILAC) coupled with mass spectrometry. This section also contains protein abundance data for both untreated and treated cells obtained from over 20 studies. These data have been normalized and converted to a common unit of molecules per cell.


Protein Half Life

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ExperimentResultReference
half-life8.7 hrChristiano R, et al. (2014)

Protein Abundance

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Abundance (molecules/cell)MediaTreatmentTreatment timeFold ChangeVisualizationStrain backgroundOriginal ReferenceReference
2618SDuntreatedconfocal microscopy evidenceS288CBreker M, et al. (2013)Ho B, et al. (2018)
2269SD1 mM hydrogen peroxide1 hrconfocal microscopy evidenceS288CBreker M, et al. (2013)Ho B, et al. (2018)
1306SD minus nitrogencellular response to nitrogen starvation15 hr0.5confocal microscopy evidenceS288CBreker M, et al. (2013)Ho B, et al. (2018)
2078SDuntreatedconfocal microscopy evidenceS288CChong YT, et al. (2015)Ho B, et al. (2018)
1792SD0.2 M hydroxyurea160 minconfocal microscopy evidenceS288CChong YT, et al. (2015)Ho B, et al. (2018)
Showing 1 to 5 of 20 entries

Domains and Classification - S288C

Collection of computationally identified domains and motifs, as determined by InterProScan analysis; includes protein coordinates for the domain, a domain Description, a Source and corresponding accession ID, and the number of S. cerevisiae genes that share the same domain.


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Gene Protein Coordinates Accession ID Description Source No. of Genes with Domain

Domain Locations

Visual representation of the locations of the domains within the protein, as listed in the Domains and Classification table. Each row displays the domain(s) derived from a different Source, with domains color-coded according to this Source.

Scroll over a domain to view its exact coordinates and its Description.

Shared Domains

This diagram displays domains (colored squares) shared between the given protein (yellow circle) and other proteins (gray circles); the domains are color-coded according to their source, as displayed in the Domain Locations table, above.

Reset

Click on a gene or domain name to go to its specific page within SGD; drag any of the gene or domain objects around within the visualization for easier viewing; click “Reset” to automatically redraw the diagram.

Alleles

Curated mutant alleles for the specified gene, listed alphabetically. Click on the allele name to open the allele page. Click "SGD search" to view all alleles in search results.


PDS5-(PCLB2) | PDS5-ECO1 | pds5-1 | pds5-AID | pds5-md | pds5-Δ

View all PDS5 alleles in SGD search

Sequence

Protein sequence for the given gene in S288C and other strains, when available. Use the pull-down menu under "Strain" to select the sequence for a specific strain. The displayed sequence can be downloaded in FASTA format as a .txt file. Amino acids displayed in blue represent modification sites. More detailed evidence for these modification sites is presented in the Post-translational Modifications table, located just below the protein sequence.


1 MAKGAVTKLK FNSPIISTSD QLISTNELLD RLKALHEELA SLDQDNTDLT GLDKYRDALV
61 SRKLLKHKDV GIRAFTACCL SDILRLYAPD APYTDAQLTD IFKLVLSQFE QLGDQENGYH
121 IQQTYLITKL LEYRSIVLLA DLPSSNNLLI ELFHIFYDPN KSFPARLFNV IGGILGEVIS
181 EFDSVPLEVL RLIFNKFLTY NPNEIPEGLN VTSDCGYEVS LILCDTYSNR MSRHLTKYYS
241 EIIHEATNDD NNSRLLTVVV KLHKLVLRLW ETVPELINAV IGFIYHELSS ENELFRKEAT
301 KLIGQILTSY SDLNFVSTHS DTFKAWISKI ADISPDVRVE WTESIPQIIA TREDISKELN
361 QALAKTFIDS DPRVRRTSVM IFNKVPVTEI WKNITNKAIY TSLLHLAREK HKEVRELCIN
421 TMAKFYSNSL NEIERTYQNK EIWEIIDTIP STLYNLYYIN DLNINEQVDS VIFEYLLPFE
481 PDNDKRVHRL LTVLSHFDKK AFTSFFAFNA RQIKISFAIS KYIDFSKFLN NQESMSSSQG
541 PIVMNKYNQT LQWLASGLSD STKAIDALET IKQFNDERIF YLLNACVTND IPFLTFKNCY
601 NELVSKLQTP GLFKKYNIST GASIMPRDIA KVIQILLFRA SPIIYNVSNI SVLLNLSNNS
661 DAKQLDLKRR ILDDISKVNP TLFKDQIRTL KTIIKDLDDP DAEKNDNLSL EEALKTLYKA
721 SKTLKDQVDF DDTFFFTKLY DFAVESKPEI TKYATKLIAL SPKAEETLKK IKIRILPLDL
781 QKDKYFTSHI IVLMEIFKKF PHVLNDDSTD IISYLIKEVL LSNQVVGDSK KEIDWVEDSL
841 LSDTKYSAIG NKVFTLKLFT NKLRSIAPDV PRDELAESFT EKTMKLFFYL IASGGELISE
901 FNKEFYPTPS NYQTKLRCVA GIQVLKLARI SNLNNFIKPS DIIKLINLVE DESLPVRKTF
961 LEQLKDYVAN ELISIKFLPL VFFTAYEPDV ELKTTTKIWI NFTFGLKSFK KGTIFERALP
1021 RLIHAIAHHP DIVGGLDSEG DAYLNALTTA IDYLLFYFDS IAAQENFSLL YYLSERVKNY
1081 QDKLVEDEID EEEGPQKEEA PKKHRPYGQK MYIIGELSQM ILLNLKEKKN WQHSAYPGKL
1141 NLPSDLFKPF ATVQEAQLSF KTYIPESLTE KIQNNIKAKI GRILHTSQTQ RQRLQKRLLA
1201 HENNESQKKK KKVHHARSQA DDEEGDGDRE SDSDDDSYSP SNKNETKKGH ENIVMKKLRV
1261 RKEVDYKDDE DDDIEMT*

* Blue amino acids indicate modification sites. More information below.

Post-translational Modifications - S288C

Modification sites for the protein in the selected strain, based on the presence of a residue in the specific strain, as inferred from experimental evidence.

25 entries for 14 sites

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SiteModificationModifierReference
S13phosphorylated residueLanz MC, et al. (2021) PMID: 33491328
K392sumoylated lysineBhagwat NR, et al. (2021) PMID: 33502312
S538phosphorylated residueAlbuquerque CP, et al. (2008) PMID: 18407956
S538phosphorylated residueSwaney DL, et al. (2013) PMID: 23749301
S538phosphorylated residueLanz MC, et al. (2021) PMID: 33491328
S761phosphorylated residueLanz MC, et al. (2021) PMID: 33491328
K763sumoylated lysineBhagwat NR, et al. (2021) PMID: 33502312
K1097sumoylated lysineBhagwat NR, et al. (2021) PMID: 33502312
K1102sumoylated lysineBhagwat NR, et al. (2021) PMID: 33502312
K1103sumoylated lysineBhagwat NR, et al. (2021) PMID: 33502312
Showing 1 to 10 of 25 entries

Sequence-Based Physico-chemical Properties - S288C

Calculated protein properties, including amino acid composition, length, coding region calculations, and atomic composition.

Amino Acid Composition

Sort table using the arrow to the right of a column header to sort by that column; download all properties as a .txt file using the "Download Properties" button.

Amino AcidFrequencyPercentage
A665.17
C80.63
D927.20
E896.97
F655.09
G342.66
H251.96
I1108.61
K1159.01
L15311.98
M131.02
N765.95
P463.60
Q443.45
R483.76
S977.60
T765.95
V614.78
W90.70
Y503.92

Physical Details

Length (a.a): 1277
Molecular Weight (Da): 147024.2
Isoelectric Point (pl): 6.18
Formula: C6662H10501N1715O1983S21
Aliphatic Index: 94.06
Instability Index: 36.91

Coding Region Translation Calculations

Codon Bias: 0.05
Codon Adaptation Index: 0.16
Frequence of Optimal Codons: 0.47
Hydropathicity of Protein: -0.32
Aromaticity Score: 0.1

Extinction Coefficients at 280nm

ALL Cys residues appear as half cystines: 124500.0
NO Cys residues appear as half cystines: 124000.0

Atomic Composition

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Atom Frequency Percentage

Data not found or not available for  S288C

External Identifiers

List of external identifiers for the protein from various database sources.

24 entries for 9 sources


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External IDSource
orf19.2216CGD
6799DIP
6323722GenBank/EMBL/DDBJ
CAA88801.1GenBank/EMBL/DDBJ
CAA89222.1GenBank/EMBL/DDBJ
Z49259GenBank/EMBL/DDBJ
Z48952GenBank/EMBL/DDBJ
2497140GenBank/EMBL/DDBJ
763023GenBank/EMBL/DDBJ
807957GenBank/EMBL/DDBJ
Showing 1 to 10 of 24 entries

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