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:ATG16L1

Protein Summary

Gene summary

Gene name: ATG16L1
ASpdb.0 ID: 55054
	Gene
Gene symbol	ATG16L1
Gene ID	55054
Gene name	autophagy related 16 like 1
Synonyms	APG16L\|ATG16A\|ATG16L\|IBD10\|WDR30
Cytomap	2q37.1
Type of gene	protein-coding
Description	autophagy-related protein 16-1APG16L betaATG16 autophagy related 16-like 1WD repeat domain 30
Modification date	20240411
UniProtAcc	Q676U5

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

Partner	Gene	GO ID	GO term	PubMed ID
Gene	ATG16L1	GO:0000421	autophagosome membrane	29317426
Gene	ATG16L1	GO:0006501	C-terminal protein lipidation	33586810
Gene	ATG16L1	GO:0016236	macroautophagy	29317426\|33586810
Gene	ATG16L1	GO:0016237	microautophagy	29317426\|33586810
Gene	ATG16L1	GO:0034274	Atg12-Atg5-Atg16 complex	29317426\|33586810
Gene	ATG16L1	GO:0036020	endolysosome membrane	29317426
Gene	ATG16L1	GO:0120095	vacuole-isolation membrane contact site	28890335

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
Q676U5-1	Q676U5-1_5nuv_A.pdb	5NUV	X-ray	1.55	A	307	607

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
Q676U5	ATG16L1	Q676U5-1	Q676U5-2	607	588	266	284	Deletion	none	none	265	265
Q676U5	ATG16L1	Q676U5-1	Q676U5-3	607	470	443	470	Substitution	IKTVFAGSSCNDIVCTEQCVMSGHFDKK	EEIQSLCLCICLDVSVEVCVCTSEPAFM	443	470
Q676U5	ATG16L1	Q676U5-1	Q676U5-3	607	470	471	607	Deletion	none	none	470	470
Q676U5	ATG16L1	Q676U5-1	Q676U5-4	607	428	70	213	Deletion	none	none	69	69
Q676U5	ATG16L1	Q676U5-1	Q676U5-4	607	428	334	368	Deletion	none	none	189	189
Q676U5	ATG16L1	Q676U5-1	Q676U5-5	607	444	70	213	Deletion	none	none	69	69
Q676U5	ATG16L1	Q676U5-1	Q676U5-5	607	444	266	284	Deletion	none	none	121	121

Multiple sequence alignment of our canonical and alternatively spliced ATG16L1

Matched gene isoform IDs with Ensembl and RefSeq of our canonical and alternative spliced genes of ATG16L1

UniProt-id	ENSG	ENST	ENSP
Q676U5-1	ENSG00000085978.22	ENST00000392017.9	ENSP00000375872.4
Q676U5-1	ENSG00000281089.3	ENST00000625501.3	ENSP00000487542.1
Q676U5-2	ENSG00000085978.22	ENST00000392020.8	ENSP00000375875.4
Q676U5-2	ENSG00000281089.3	ENST00000630066.2	ENSP00000487446.1
Q676U5-4	ENSG00000085978.22	ENST00000373525.9	ENSP00000362625.5
Q676U5-4	ENSG00000281089.3	ENST00000630204.2	ENSP00000487455.1
Q676U5-5	ENSG00000085978.22	ENST00000347464.9	ENSP00000318259.6
Q676U5-5	ENSG00000281089.3	ENST00000626623.2	ENSP00000487298.1

UniProt-id	NM ID	NP ID
Q676U5-1	NM_030803.6	NP_110430.5
Q676U5-2	NM_017974.3	NP_060444.3
Q676U5-5	NM_198890.2	NP_942593.2

Amino acid sequences of our canonical and alternatively spliced ATG16L1

accession_id	Protein sequence
Q676U5-1	MSSGLRAADFPRWKRHISEQLRRRDRLQRQAFEEIILQYNKLLEKSDLHSVLAQKLQAEKHDVPNRHEISPGHDGTWNDNQLQEMAQLRI KHQEELTELHKKRGELAQLVIDLNNQMQRKDREMQMNEAKIAECLQTISDLETECLDLRTKLCDLERANQTLKDEYDALQITFTALEGKL RKTTEENQELVTRWMAEKAQEANRLNAENEKDSRRRQARLQKELAEAAKEPLPVEQDDDIEVIVDETSDHTEETSPVRAISRAATKRLSQ PAGGLLDSITNIFGRRSVSSFPVPQDNVDTHPGSGKEVRVPATALCVFDAHDGEVNAVQFSPGSRLLATGGMDRRVKLWEVFGEKCEFKG SLSGSNAGITSIEFDSAGSYLLAASNDFASRIWTVDDYRLRHTLTGHSGKVLSAKFLLDNARIVSGSHDRTLKLWDLRSKVCIKTVFAGS SCNDIVCTEQCVMSGHFDKKIRFWDIRSESIVREMELLGKITALDLNPERTELLSCSRDDLLKVIDLRTNAIKQTFSAPGFKCGSDWTRV
Q676U5-2	MSSGLRAADFPRWKRHISEQLRRRDRLQRQAFEEIILQYNKLLEKSDLHSVLAQKLQAEKHDVPNRHEISPGHDGTWNDNQLQEMAQLRI KHQEELTELHKKRGELAQLVIDLNNQMQRKDREMQMNEAKIAECLQTISDLETECLDLRTKLCDLERANQTLKDEYDALQITFTALEGKL RKTTEENQELVTRWMAEKAQEANRLNAENEKDSRRRQARLQKELAEAAKEPLPVEQDDDIEVIVDETSDHTEETSPVRAISRAATRRSVS SFPVPQDNVDTHPGSGKEVRVPATALCVFDAHDGEVNAVQFSPGSRLLATGGMDRRVKLWEVFGEKCEFKGSLSGSNAGITSIEFDSAGS YLLAASNDFASRIWTVDDYRLRHTLTGHSGKVLSAKFLLDNARIVSGSHDRTLKLWDLRSKVCIKTVFAGSSCNDIVCTEQCVMSGHFDK KIRFWDIRSESIVREMELLGKITALDLNPERTELLSCSRDDLLKVIDLRTNAIKQTFSAPGFKCGSDWTRVVFSPDGSYVAAGSAEGSLY
Q676U5-3	MSSGLRAADFPRWKRHISEQLRRRDRLQRQAFEEIILQYNKLLEKSDLHSVLAQKLQAEKHDVPNRHEISPGHDGTWNDNQLQEMAQLRI KHQEELTELHKKRGELAQLVIDLNNQMQRKDREMQMNEAKIAECLQTISDLETECLDLRTKLCDLERANQTLKDEYDALQITFTALEGKL RKTTEENQELVTRWMAEKAQEANRLNAENEKDSRRRQARLQKELAEAAKEPLPVEQDDDIEVIVDETSDHTEETSPVRAISRAATKRLSQ PAGGLLDSITNIFGRRSVSSFPVPQDNVDTHPGSGKEVRVPATALCVFDAHDGEVNAVQFSPGSRLLATGGMDRRVKLWEVFGEKCEFKG SLSGSNAGITSIEFDSAGSYLLAASNDFASRIWTVDDYRLRHTLTGHSGKVLSAKFLLDNARIVSGSHDRTLKLWDLRSKVCEEIQSLCL
Q676U5-4	MSSGLRAADFPRWKRHISEQLRRRDRLQRQAFEEIILQYNKLLEKSDLHSVLAQKLQAEKHDVPNRHEIRRRQARLQKELAEAAKEPLPV EQDDDIEVIVDETSDHTEETSPVRAISRAATKRLSQPAGGLLDSITNIFGRRSVSSFPVPQDNVDTHPGSGKEVRVPATALCVFDAHDGE VNAVQFSPGITSIEFDSAGSYLLAASNDFASRIWTVDDYRLRHTLTGHSGKVLSAKFLLDNARIVSGSHDRTLKLWDLRSKVCIKTVFAG SSCNDIVCTEQCVMSGHFDKKIRFWDIRSESIVREMELLGKITALDLNPERTELLSCSRDDLLKVIDLRTNAIKQTFSAPGFKCGSDWTR
Q676U5-5	MSSGLRAADFPRWKRHISEQLRRRDRLQRQAFEEIILQYNKLLEKSDLHSVLAQKLQAEKHDVPNRHEIRRRQARLQKELAEAAKEPLPV EQDDDIEVIVDETSDHTEETSPVRAISRAATRRSVSSFPVPQDNVDTHPGSGKEVRVPATALCVFDAHDGEVNAVQFSPGSRLLATGGMD RRVKLWEVFGEKCEFKGSLSGSNAGITSIEFDSAGSYLLAASNDFASRIWTVDDYRLRHTLTGHSGKVLSAKFLLDNARIVSGSHDRTLK LWDLRSKVCIKTVFAGSSCNDIVCTEQCVMSGHFDKKIRFWDIRSESIVREMELLGKITALDLNPERTELLSCSRDDLLKVIDLRTNAIK

Protein Functional Features

Main function of this protein. (from UniProt)

ATG16L1 (go to UniProt):Q676U5

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
Q676U5	Repeat	320	359	Note=WD 1;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00221	Type=Deletion;Start=334;End=368
Q676U5	Repeat	364	403	Note=WD 2;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00221	Type=Deletion;Start=334;End=368
Q676U5	Repeat	406	445	Note=WD 3;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00221	Type=Substitution;Start=443;End=470
Q676U5	Repeat	447	484	Note=WD 4;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00221	Type=Substitution;Start=443;End=470
Q676U5	Repeat	447	484	Note=WD 4;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00221	Type=Deletion;Start=471;End=607
Q676U5	Repeat	486	525	Note=WD 5;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00221	Type=Deletion;Start=471;End=607
Q676U5	Repeat	532	573	Note=WD 6;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00221	Type=Deletion;Start=471;End=607
Q676U5	Repeat	575	607	Note=WD 7;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00221	Type=Deletion;Start=471;End=607
Q676U5	Region	207	230	Note=WIPI2-binding;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:24954904;Dbxref=PMID:24954904	Type=Deletion;Start=70;End=213
Q676U5	Region	207	230	Note=WIPI2-binding;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:24954904;Dbxref=PMID:24954904	Type=Deletion;Start=70;End=213
Q676U5	Coiled coil	78	230	Ontology_term=ECO:0000255;evidence=ECO:0000255	Type=Deletion;Start=70;End=213
Q676U5	Coiled coil	78	230	Ontology_term=ECO:0000255;evidence=ECO:0000255	Type=Deletion;Start=70;End=213

Gene Isoform Structures and Expression Levels for ATG16L1

Gene structures of our canonical and alternative spliced genes of ATG16L1
* 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 Q676U5-1

3D view using mol* of Q676U5-2

3D view using mol* of Q676U5-3

3D view using mol* of Q676U5-4

3D view using mol* of Q676U5-5

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 Q676U5-1

pLDDT distribution across the protein length of Q676U5-2

pLDDT distribution across the protein length of Q676U5-3

pLDDT distribution across the protein length of Q676U5-4

pLDDT distribution across the protein length of Q676U5-5

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 Q676U5-1

Ramachandran plot of Q676U5-2

Ramachandran plot of Q676U5-3

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
Q676U5-1	1.262	78	1.359	78.89	0.179	0.96	1.277	7.151	0.144	49.647	0.254	417,422,424,432,433,434,444,446,462,474,475,476,47 9
Q676U5-2	1.239	75	1.328	74.431	0.235	0.956	1.242	7.153	0.184	38.972	0.914	398,403,405,413,414,415,425,427,443,455,456,457,46 0
Q676U5-3	1.012	102	1.061	661.99	0.726	0.657	0.82	0.502	0.838	0.599	0.89	329,330,332,373,374,375,376,412,413,415,416,417,41 8,420,424,425,426,427,428,430,431,432,447,448,449, 450,451,452,453,454,455,456,458,460,461,462
Q676U5-4	1.262	72	1.363	80.262	0.172	0.973	1.291	7.676	0.055	139.868	4.432	238,245,253,254,255,265,267,283,295,296,297,300
Q676U5-5	1.252	74	1.347	75.46	0.169	0.964	1.276	7.151	0.123	58.25	1.165	254,259,261,269,270,271,281,283,299,311,312,313,31 4,316

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 Q676U5-1_Q676U5-1_5nuv_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 Q676U5-1_5nuv_A_Q676U5-2.pdb

3D view using mol* of Q676U5-1_5nuv_A_Q676U5-3.pdb

3D view using mol* of Q676U5-1_5nuv_A_Q676U5-4.pdb

3D view using mol* of Q676U5-1_5nuv_A_Q676U5-5.pdb

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

3D view using mol* of Q676U5-1_Q676U5-2.pdb

3D view using mol* of Q676U5-1_Q676U5-3.pdb

3D view using mol* of Q676U5-1_Q676U5-4.pdb

3D view using mol* of Q676U5-1_Q676U5-5.pdb

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

./stats/secondary_structure/figure/Q676U5-1_vs_Q676U5-2.png