ASpdb: an integrative knowledgebase of human protein isoforms from experimental and AI-predicted structures

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	Protein Summary
	AS Summary
	Protein Functional Features
	Gene Isoform Structures and Expression Levels
	Protein Structures
	pLDDT Score Distribution
	Ramachandran Plot of Protein Structures
	Potential Active Site Information
	Protein Structure and Feature Comparision
	Protein-Protein Interaction
	Related Drugs
	Related Diseases
	Clinically Important Variants

Protein:ATG13

Protein Summary

Gene summary

Gene name: ATG13
ASpdb.0 ID: 9776
	Gene
Gene symbol	ATG13
Gene ID	9776
Gene name	autophagy related 13
Synonyms	KIAA0652\|PARATARG8
Cytomap	11p11.2
Type of gene	protein-coding
Description	autophagy-related protein 13ATG13 autophagy related 13 homolog
Modification date	20240407
UniProtAcc	O75143

Gene ontology of this gene with evidence of Inferred from Direct Assay (IDA) from Entrez

Partner	Gene	GO ID	GO term	PubMed ID
Gene	ATG13	GO:0000045	autophagosome assembly	19225151
Gene	ATG13	GO:0000407	phagophore assembly site	19597335
Gene	ATG13	GO:0005739	mitochondrion	21855797
Gene	ATG13	GO:0008285	negative regulation of cell population proliferation	21795849
Gene	ATG13	GO:0010508	positive regulation of autophagy	29487085
Gene	ATG13	GO:0019901	protein kinase binding	29487085
Gene	ATG13	GO:0034045	phagophore assembly site membrane	19597335
Gene	ATG13	GO:0043539	protein serine/threonine kinase activator activity	19225151
Gene	ATG13	GO:1903059	regulation of protein lipidation	19225151

AS Summary

Information of the canonical protein with experimentally identified structure from PDB (2023).

UniProt Acc	File name	PDB ID	Method	Resolution	Chain	Start	End
O75143-1	O75143-1_5xv6_A.pdb	5XV6	X-ray	2.46	A	4	190

ASpdb's canonical and alternatively spliced isoform information.

accession_id	gene_name	canonical_id	alternative_id	canonical_length	alternative_length	canonical_start	canonical_end	type	originalSEQ	variationSEQ	alternative_start	alternative_end
O75143	ATG13	O75143-1	O75143-2	517	480	265	301	Deletion	none	none	264	264
O75143	ATG13	O75143-1	O75143-3	517	405	265	301	Deletion	none	none	264	264
O75143	ATG13	O75143-1	O75143-3	517	405	428	442	Substitution	HSDGSSGGSSGNTHD	PCSWPLPCLLSPSTV	391	405
O75143	ATG13	O75143-1	O75143-3	517	405	443	517	Deletion	none	none	405	405
O75143	ATG13	O75143-1	O75143-4	517	401	1	79	Deletion	none	none	0	0
O75143	ATG13	O75143-1	O75143-4	517	401	263	299	Deletion	none	none	183	183
O75143	ATG13	O75143-1	O75143-5	517	550	262	262	Substitution	S	SQCVFTVTKAHFQTPTPVVTDTLRVPMAGLAFSH	262	295

Multiple sequence alignment of our canonical and alternatively spliced ATG13

Matched gene isoform IDs with Ensembl and RefSeq of our canonical and alternative spliced genes of ATG13

UniProt-id	ENSG	ENST	ENSP
O75143-1	ENSG00000175224.17	ENST00000359513.8	ENSP00000352500.4
O75143-1	ENSG00000175224.17	ENST00000526508.5	ENSP00000431974.1
O75143-2	ENSG00000175224.17	ENST00000524625.5	ENSP00000433543.1
O75143-2	ENSG00000175224.17	ENST00000529655.5	ENSP00000433756.1
O75143-4	ENSG00000175224.17	ENST00000530500.5	ENSP00000434390.1
O75143-5	ENSG00000175224.17	ENST00000528494.5	ENSP00000432412.1
O75143-5	ENSG00000175224.17	ENST00000683050.1	ENSP00000507809.1

UniProt-id	NM ID	NP ID
O75143-1	NM_001142673.2	NP_001136145.1
O75143-1	NM_001205120.1	NP_001192049.1
O75143-1	NM_001346319.1	NP_001333248.1
O75143-1	NM_001346320.1	NP_001333249.1
O75143-1	NM_001346321.1	NP_001333250.1
O75143-1	NM_001346322.1	NP_001333251.1
O75143-1	NM_001346323.1	NP_001333252.1
O75143-1	NM_001346324.1	NP_001333253.1
O75143-1	NM_001346325.1	NP_001333254.1
O75143-1	NM_001346326.1	NP_001333255.1
O75143-1	NM_001346327.1	NP_001333256.1
O75143-1	NM_001346328.1	NP_001333257.1
O75143-1	NM_001346329.1	NP_001333258.1
O75143-1	NM_001346330.1	NP_001333259.1
O75143-1	NM_001346331.1	NP_001333260.1
O75143-1	NM_001346332.1	NP_001333261.1
O75143-2	NM_001205121.1	NP_001192050.1
O75143-2	NM_001346342.1	NP_001333271.1
O75143-2	NM_001346344.1	NP_001333273.1
O75143-2	NM_001346346.1	NP_001333275.1
O75143-2	NM_001346348.1	NP_001333277.1
O75143-2	NM_001346349.1	NP_001333278.1
O75143-2	NM_001346350.1	NP_001333279.1
O75143-2	NM_001346351.1	NP_001333280.1
O75143-2	NM_001346352.1	NP_001333281.1
O75143-2	NM_001346353.1	NP_001333282.1
O75143-2	NM_001346354.1	NP_001333283.1
O75143-2	NM_014741.4	NP_055556.2
O75143-4	NM_001205122.1	NP_001192051.1
O75143-5	NM_001205119.1	NP_001192048.1
O75143-5	NM_001346311.1	NP_001333240.1
O75143-5	NM_001346312.1	NP_001333241.1
O75143-5	NM_001346313.1	NP_001333242.1
O75143-5	NM_001346314.1	NP_001333243.1
O75143-5	NM_001346315.1	NP_001333244.1
O75143-5	NM_001346316.1	NP_001333245.1

Amino acid sequences of our canonical and alternatively spliced ATG13

accession_id	Protein sequence
O75143-1	METDLNSQDRKDLDKFIKFFALKTVQVIVQARLGEKICTRSSSSPTGSDWFNLAIKDIPEVTHEAKKALAGQLPAVGRSMCVEISLKTSE GDSMELEIWCLEMNEKCDKEIKVSYTVYNRLSLLLKSLLAITRVTPAYRLSRKQGHEYVILYRIYFGEVQLSGLGEGFQTVRVGTVGTPV GTITLSCAYRINLAFMSTRQFERTPPIMGIIIDHFVDRPYPSSSPMHPCNYRTAGEDTGVIYPSVEDSQEVCTTSFSTSPPSQLSSSRLS YQPAALGVGSADLAYPVVFAAGLNATHPHQLMVPGKEGGVPLAPNQPVHGTQADQERLATCTPSDRTHCAATPSSSEDTETVSNSSEGRA SPHDVLETIFVRKVGAFVNKPINQVTLTSLDIPFAMFAPKNLELEDTDPMVNPPDSPETESPLQGSLHSDGSSGGSSGNTHDDFVMIDFK
O75143-2	METDLNSQDRKDLDKFIKFFALKTVQVIVQARLGEKICTRSSSSPTGSDWFNLAIKDIPEVTHEAKKALAGQLPAVGRSMCVEISLKTSE GDSMELEIWCLEMNEKCDKEIKVSYTVYNRLSLLLKSLLAITRVTPAYRLSRKQGHEYVILYRIYFGEVQLSGLGEGFQTVRVGTVGTPV GTITLSCAYRINLAFMSTRQFERTPPIMGIIIDHFVDRPYPSSSPMHPCNYRTAGEDTGVIYPSVEDSQEVCTTSFSTSPPSQLMVPGKE GGVPLAPNQPVHGTQADQERLATCTPSDRTHCAATPSSSEDTETVSNSSEGRASPHDVLETIFVRKVGAFVNKPINQVTLTSLDIPFAMF APKNLELEDTDPMVNPPDSPETESPLQGSLHSDGSSGGSSGNTHDDFVMIDFKPAFSKDDILPMDLGTFYREFQNPPQLSSLSIDIGAQS
O75143-3	METDLNSQDRKDLDKFIKFFALKTVQVIVQARLGEKICTRSSSSPTGSDWFNLAIKDIPEVTHEAKKALAGQLPAVGRSMCVEISLKTSE GDSMELEIWCLEMNEKCDKEIKVSYTVYNRLSLLLKSLLAITRVTPAYRLSRKQGHEYVILYRIYFGEVQLSGLGEGFQTVRVGTVGTPV GTITLSCAYRINLAFMSTRQFERTPPIMGIIIDHFVDRPYPSSSPMHPCNYRTAGEDTGVIYPSVEDSQEVCTTSFSTSPPSQLMVPGKE GGVPLAPNQPVHGTQADQERLATCTPSDRTHCAATPSSSEDTETVSNSSEGRASPHDVLETIFVRKVGAFVNKPINQVTLTSLDIPFAMF
O75143-4	MCVEISLKTSEGDSMELEIWCLEMNEKCDKEIKVSYTVYNRLSLLLKSLLAITRVTPAYRLSRKQGHEYVILYRIYFGEVQLSGLGEGFQ TVRVGTVGTPVGTITLSCAYRINLAFMSTRQFERTPPIMGIIIDHFVDRPYPSSSPMHPCNYRTAGEDTGVIYPSVEDSQEVCTTSFSTS PPSQLMVPGKEGGVPLAPNQPVHGTQADQERLATCTPSDRTHCAATPSSSEDTETVSNSSEGRASPHDVLETIFVRKVGAFVNKPINQVT LTSLDIPFAMFAPKNLELEDTDPMVNPPDSPETESPLQGSLHSDGSSGGSSGNTHDDFVMIDFKPAFSKDDILPMDLGTFYREFQNPPQL
O75143-5	METDLNSQDRKDLDKFIKFFALKTVQVIVQARLGEKICTRSSSSPTGSDWFNLAIKDIPEVTHEAKKALAGQLPAVGRSMCVEISLKTSE GDSMELEIWCLEMNEKCDKEIKVSYTVYNRLSLLLKSLLAITRVTPAYRLSRKQGHEYVILYRIYFGEVQLSGLGEGFQTVRVGTVGTPV GTITLSCAYRINLAFMSTRQFERTPPIMGIIIDHFVDRPYPSSSPMHPCNYRTAGEDTGVIYPSVEDSQEVCTTSFSTSPPSQCVFTVTK AHFQTPTPVVTDTLRVPMAGLAFSHQLSSSRLSYQPAALGVGSADLAYPVVFAAGLNATHPHQLMVPGKEGGVPLAPNQPVHGTQADQER LATCTPSDRTHCAATPSSSEDTETVSNSSEGRASPHDVLETIFVRKVGAFVNKPINQVTLTSLDIPFAMFAPKNLELEDTDPMVNPPDSP ETESPLQGSLHSDGSSGGSSGNTHDDFVMIDFKPAFSKDDILPMDLGTFYREFQNPPQLSSLSIDIGAQSMAEDLDSLPEKLAVHEKNVR

Protein Functional Features

Main function of this protein. (from UniProt)

ATG13 (go to UniProt):O75143

Retention analysis result of protein across 39 protein features of UniProt such as six molecule processing features, 13 region features, four site features, six amino acid modification features, two natural variation features, five experimental info features, and 3 secondary structure features. Here, because of limited space for viewing, we only show the protein feature retention information belong to the 13 regional features. All retention annotation result can be downloaded at
download page
* Minus value of BPloci means that the break pointn is located before the CDS.

- Retained protein feature among the 13 regional features.

Accession_id	Subsection	Start	End	Funcitonal feature	Splicing information
O75143	Region	405	439	Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Substitution;Start=428;End=442
O75143	Motif	444	447	Note=LIR;Ontology_term=ECO:0000305;evidence=ECO:0000305\|PubMed:24290141;Dbxref=PMID:24290141	Type=Deletion;Start=443;End=517
O75143	Compositional bias	417	439	Note=Polar residues;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Substitution;Start=428;End=442

Gene Isoform Structures and Expression Levels for ATG13

Gene structures of our canonical and alternative spliced genes of ATG13
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

Expression levels of gene isoforms across GTEx.

Expression levels of gene isoforms across TCGA.

Protein Structures

PDB and CIF files of the predicted protein structures
* Here we show the 3D structure of the proteins using Mol*. AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. Model confidence is shown from the pLDDT values per residue. pLDDT corresponds to the model’s prediction of its score on the local Distance Difference Test. It is a measure of local accuracy (from AlphfaFold website). To color code individual residues, we transformed individual PDB files into CIF format.

3D view using mol* of O75143-1

3D view using mol* of O75143-2

3D view using mol* of O75143-3

3D view using mol* of O75143-4

3D view using mol* of O75143-5

pLDDT Score Distribution

pLDDT score distribution of the predicted protein structures from AlphaFold2
* AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100.

pLDDT distribution across the protein length of O75143-1

pLDDT distribution across the protein length of O75143-2

pLDDT distribution across the protein length of O75143-3

pLDDT distribution across the protein length of O75143-4

pLDDT distribution across the protein length of O75143-5

Ramachandran Plot of Protein Structures

Ramachandran plot of the torsional angles - phi (φ)and psi (ψ) - of the residues (amino acids) contained in this protein peptide.

Ramachandran plot of O75143-1

Ramachandran plot of O75143-2

Ramachandran plot of O75143-3

Ramachandran plot of O75143-4

Potential Active Site Information

The potential binding sites of these proteins were identified using SiteMap, a module of the Schrodinger suite.

UniProt-id	Site score	Size	D score	Volume	Exposure	Enclosure	Contact	Phobic	Philic	Balance	Don/Acc	Residues
O75143-1	0.907	89	0.945	231.182	0.744	0.575	0.71	0.431	0.878	0.491	0.571	23,27,30,31,35,36,37,38,39,40,41,42,45,48,49,52,53 ,54,55,56,57,129,133,138
O75143-2	1.029	136	1.075	489.461	0.529	0.686	0.913	0.546	0.848	0.644	1.475	29,32,33,58,60,61,64,83,85,144,149,150,151,152,153 ,154,252,253,254,255,256,257
O75143-3	0.985	307	1.021	673.309	0.558	0.646	0.848	0.753	0.939	0.801	0.839	33,34,35,86,88,89,90,92,94,96,136,140,141,142,143, 144,145,146,147,148,192,193,194,195,196,197,198,19 9,338,339,340,341,342,343,345,348,349,350,351,352, 353,354,355,356,357,360
O75143-4	1.12	88	1.186	308.7	0.503	0.801	1.05	2.011	0.541	3.715	0.546	1,3,5,17,18,20,21,22,46,49,53,54,56,58,59,62,65,71 ,73,106,259,260,261
O75143-5	0.818	59	0.82	184.534	0.722	0.624	0.814	0.895	0.849	1.055	0.503	27,30,31,35,36,37,39,40,41,42,45,49,52,53,54,55,56 ,129,133,138

Protein Structure and Feature Comparision

Protein Structure Comparision Using Template Modeling Scores (TM-score).

Protein Structure Comparision Visualization with mol*. between Canonical predicted structure (AF2)(orange) vs Canonical validated structure (PDB)(green)

3D view using mol* of O75143-1_O75143-1_5xv6_A.pdb

Protein Structure Comparision Visualization with mol*. between Canonical validated structure (PDB)(orange) vs Alternative predicted structure (AF2)(green)

3D view using mol* of O75143-1_5xv6_A_O75143-2.pdb

3D view using mol* of O75143-1_5xv6_A_O75143-3.pdb

3D view using mol* of O75143-1_5xv6_A_O75143-4.pdb

3D view using mol* of O75143-1_5xv6_A_O75143-5.pdb

Protein Structure Comparision Visualization with mol*. between Canonical predicted structure (AF2)(orange) vs Alternative predicted structure (AF2)(green)

3D view using mol* of O75143-1_O75143-2.pdb

3D view using mol* of O75143-1_O75143-3.pdb

3D view using mol* of O75143-1_O75143-4.pdb

3D view using mol* of O75143-1_O75143-5.pdb

Protein Feature Comparison of the protein sequendary structures among the protiens.

./stats/secondary_structure/figure/O75143-1_vs_O75143-2.png