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:PTPN22

Protein Summary

Gene summary

Gene name: PTPN22
ASpdb.0 ID: 26191
	Gene
Gene symbol	PTPN22
Gene ID	26191
Gene name	protein tyrosine phosphatase non-receptor type 22
Synonyms	LYP\|LYP1\|LYP2\|PEP\|PTPN22.5\|PTPN22.6\|PTPN8
Cytomap	1p13.2
Type of gene	protein-coding
Description	tyrosine-protein phosphatase non-receptor type 22PEST-domain phosphatasehematopoietic cell protein-tyrosine phosphatase 70Z-PEPlymphoid-specific protein tyrosine phosphataseprotein tyrosine phosphatase, non-receptor type 22 (lymphoid)protein tyrosine
Modification date	20240411
UniProtAcc	Q9Y2R2

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

Partner	Gene	GO ID	GO term	PubMed ID
Gene	PTPN22	GO:0004725	protein tyrosine phosphatase activity	10068674\|16461343\|18056643\|27043286
Gene	PTPN22	GO:0005634	nucleus	10940933
Gene	PTPN22	GO:0005737	cytoplasm	10068674\|10940933
Gene	PTPN22	GO:0006470	protein dephosphorylation	10068674
Gene	PTPN22	GO:0009898	cytoplasmic side of plasma membrane	10940933
Gene	PTPN22	GO:0016791	phosphatase activity	23991106
Gene	PTPN22	GO:0032817	regulation of natural killer cell proliferation	20522204
Gene	PTPN22	GO:0048471	perinuclear region of cytoplasm	10068674
Gene	PTPN22	GO:0050860	negative regulation of T cell receptor signaling pathway	18056643
Gene	PTPN22	GO:0071225	cellular response to muramyl dipeptide	23991106
Gene	PTPN22	GO:1900227	positive regulation of NLRP3 inflammasome complex assembly	27043286

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
Q9Y2R2-1	Q9Y2R2-1_4j51_A.pdb	4J51	X-ray	2.3	A	1	303

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
Q9Y2R2	PTPN22	Q9Y2R2-1	Q9Y2R2-2	807	691	685	807	Substitution	ELHQDRSSPPPPLPERTLESFFLADEDCMQAQSIETYSTSYPDTMENSTSSKQTLKTPGKSFTRSKSLKILRNMKKSICNSCPPNKPAESVQSNNSSSFLNFGFANRFSKPKGPRNPPPTWNI	GKNFSWL	685	691
Q9Y2R2	PTPN22	Q9Y2R2-1	Q9Y2R2-3	807	752	251	305	Deletion	none	none	250	250
Q9Y2R2	PTPN22	Q9Y2R2-1	Q9Y2R2-4	807	779	647	674	Deletion	none	none	646	646
Q9Y2R2	PTPN22	Q9Y2R2-1	Q9Y2R2-5	807	179	137	160	Deletion	none	none	136	136
Q9Y2R2	PTPN22	Q9Y2R2-1	Q9Y2R2-5	807	179	181	203	Substitution	ETRTIYQFHYKNWPDHDVPSSID	VSVILAHQTSLQNLFSQITPAHF	157	179
Q9Y2R2	PTPN22	Q9Y2R2-1	Q9Y2R2-5	807	179	204	807	Deletion	none	none	179	179
Q9Y2R2	PTPN22	Q9Y2R2-1	Q9Y2R2-6	807	668	124	250	Deletion	none	none	123	123
Q9Y2R2	PTPN22	Q9Y2R2-1	Q9Y2R2-6	807	668	788	807	Substitution	FANRFSKPKGPRNPPPTWNI	MCVILLKS	661	668

Multiple sequence alignment of our canonical and alternatively spliced PTPN22

Matched gene isoform IDs with Ensembl and RefSeq of our canonical and alternative spliced genes of PTPN22

UniProt-id	ENSG	ENST	ENSP
Q9Y2R2-5	ENSG00000134242.16	ENST00000460620.5	ENSP00000433141.1

UniProt-id	NM ID	NP ID
Q9Y2R2-3	NM_012411.5	NP_036543.4
Q9Y2R2-4	NM_001193431.2	NP_001180360.1

Amino acid sequences of our canonical and alternatively spliced PTPN22

accession_id	Protein sequence
Q9Y2R2-1	MDQREILQKFLDEAQSKKITKEEFANEFLKLKRQSTKYKADKTYPTTVAEKPKNIKKNRYKDILPYDYSRVELSLITSDEDSSYINANFI KGVYGPKAYIATQGPLSTTLLDFWRMIWEYSVLIIVMACMEYEMGKKKCERYWAEPGEMQLEFGPFSVSCEAEKRKSDYIIRTLKVKFNS ETRTIYQFHYKNWPDHDVPSSIDPILELIWDVRCYQEDDSVPICIHCSAGCGRTGVICAIDYTWMLLKDGIIPENFSVFSLIREMRTQRP SLVQTQEQYELVYNAVLELFKRQMDVIRDKHSGTESQAKHCIPEKNHTLQADSYSPNLPKSTTKAAKMMNQQRTKMEIKESSSFDFRTSE ISAKEELVLHPAKSSTSFDFLELNYSFDKNADTTMKWQTKAFPIVGEPLQKHQSLDLGSLLFEGCSNSKPVNAAGRYFNSKVPITRTKST PFELIQQRETKEVDSKENFSYLESQPHDSCFVEMQAQKVMHVSSAELNYSLPYDSKHQIRNASNVKHHDSSALGVYSYIPLVENPYFSSW PPSGTSSKMSLDLPEKQDGTVFPSSLLPTSSTSLFSYYNSHDSLSLNSPTNISSLLNQESAVLATAPRIDDEIPPPLPVRTPESFIVVEE AGEFSPNVPKSLSSAVKVKIGTSLEWGGTSEPKKFDDSVILRPSKSVKLRSPKSELHQDRSSPPPPLPERTLESFFLADEDCMQAQSIET
Q9Y2R2-2	MDQREILQKFLDEAQSKKITKEEFANEFLKLKRQSTKYKADKTYPTTVAEKPKNIKKNRYKDILPYDYSRVELSLITSDEDSSYINANFI KGVYGPKAYIATQGPLSTTLLDFWRMIWEYSVLIIVMACMEYEMGKKKCERYWAEPGEMQLEFGPFSVSCEAEKRKSDYIIRTLKVKFNS ETRTIYQFHYKNWPDHDVPSSIDPILELIWDVRCYQEDDSVPICIHCSAGCGRTGVICAIDYTWMLLKDGIIPENFSVFSLIREMRTQRP SLVQTQEQYELVYNAVLELFKRQMDVIRDKHSGTESQAKHCIPEKNHTLQADSYSPNLPKSTTKAAKMMNQQRTKMEIKESSSFDFRTSE ISAKEELVLHPAKSSTSFDFLELNYSFDKNADTTMKWQTKAFPIVGEPLQKHQSLDLGSLLFEGCSNSKPVNAAGRYFNSKVPITRTKST PFELIQQRETKEVDSKENFSYLESQPHDSCFVEMQAQKVMHVSSAELNYSLPYDSKHQIRNASNVKHHDSSALGVYSYIPLVENPYFSSW PPSGTSSKMSLDLPEKQDGTVFPSSLLPTSSTSLFSYYNSHDSLSLNSPTNISSLLNQESAVLATAPRIDDEIPPPLPVRTPESFIVVEE
Q9Y2R2-3	MDQREILQKFLDEAQSKKITKEEFANEFLKLKRQSTKYKADKTYPTTVAEKPKNIKKNRYKDILPYDYSRVELSLITSDEDSSYINANFI KGVYGPKAYIATQGPLSTTLLDFWRMIWEYSVLIIVMACMEYEMGKKKCERYWAEPGEMQLEFGPFSVSCEAEKRKSDYIIRTLKVKFNS ETRTIYQFHYKNWPDHDVPSSIDPILELIWDVRCYQEDDSVPICIHCSAGCGRTGVICAIDYTWMLLKDGSQAKHCIPEKNHTLQADSYS PNLPKSTTKAAKMMNQQRTKMEIKESSSFDFRTSEISAKEELVLHPAKSSTSFDFLELNYSFDKNADTTMKWQTKAFPIVGEPLQKHQSL DLGSLLFEGCSNSKPVNAAGRYFNSKVPITRTKSTPFELIQQRETKEVDSKENFSYLESQPHDSCFVEMQAQKVMHVSSAELNYSLPYDS KHQIRNASNVKHHDSSALGVYSYIPLVENPYFSSWPPSGTSSKMSLDLPEKQDGTVFPSSLLPTSSTSLFSYYNSHDSLSLNSPTNISSL LNQESAVLATAPRIDDEIPPPLPVRTPESFIVVEEAGEFSPNVPKSLSSAVKVKIGTSLEWGGTSEPKKFDDSVILRPSKSVKLRSPKSE LHQDRSSPPPPLPERTLESFFLADEDCMQAQSIETYSTSYPDTMENSTSSKQTLKTPGKSFTRSKSLKILRNMKKSICNSCPPNKPAESV
Q9Y2R2-4	MDQREILQKFLDEAQSKKITKEEFANEFLKLKRQSTKYKADKTYPTTVAEKPKNIKKNRYKDILPYDYSRVELSLITSDEDSSYINANFI KGVYGPKAYIATQGPLSTTLLDFWRMIWEYSVLIIVMACMEYEMGKKKCERYWAEPGEMQLEFGPFSVSCEAEKRKSDYIIRTLKVKFNS ETRTIYQFHYKNWPDHDVPSSIDPILELIWDVRCYQEDDSVPICIHCSAGCGRTGVICAIDYTWMLLKDGIIPENFSVFSLIREMRTQRP SLVQTQEQYELVYNAVLELFKRQMDVIRDKHSGTESQAKHCIPEKNHTLQADSYSPNLPKSTTKAAKMMNQQRTKMEIKESSSFDFRTSE ISAKEELVLHPAKSSTSFDFLELNYSFDKNADTTMKWQTKAFPIVGEPLQKHQSLDLGSLLFEGCSNSKPVNAAGRYFNSKVPITRTKST PFELIQQRETKEVDSKENFSYLESQPHDSCFVEMQAQKVMHVSSAELNYSLPYDSKHQIRNASNVKHHDSSALGVYSYIPLVENPYFSSW PPSGTSSKMSLDLPEKQDGTVFPSSLLPTSSTSLFSYYNSHDSLSLNSPTNISSLLNQESAVLATAPRIDDEIPPPLPVRTPESFIVVEE AGEFSPNVPKSLSSAVKSVKLRSPKSELHQDRSSPPPPLPERTLESFFLADEDCMQAQSIETYSTSYPDTMENSTSSKQTLKTPGKSFTR
Q9Y2R2-5	MDQREILQKFLDEAQSKKITKEEFANEFLKLKRQSTKYKADKTYPTTVAEKPKNIKKNRYKDILPYDYSRVELSLITSDEDSSYINANFI
Q9Y2R2-6	MDQREILQKFLDEAQSKKITKEEFANEFLKLKRQSTKYKADKTYPTTVAEKPKNIKKNRYKDILPYDYSRVELSLITSDEDSSYINANFI KGVYGPKAYIATQGPLSTTLLDFWRMIWEYSVLIIPENFSVFSLIREMRTQRPSLVQTQEQYELVYNAVLELFKRQMDVIRDKHSGTESQ AKHCIPEKNHTLQADSYSPNLPKSTTKAAKMMNQQRTKMEIKESSSFDFRTSEISAKEELVLHPAKSSTSFDFLELNYSFDKNADTTMKW QTKAFPIVGEPLQKHQSLDLGSLLFEGCSNSKPVNAAGRYFNSKVPITRTKSTPFELIQQRETKEVDSKENFSYLESQPHDSCFVEMQAQ KVMHVSSAELNYSLPYDSKHQIRNASNVKHHDSSALGVYSYIPLVENPYFSSWPPSGTSSKMSLDLPEKQDGTVFPSSLLPTSSTSLFSY YNSHDSLSLNSPTNISSLLNQESAVLATAPRIDDEIPPPLPVRTPESFIVVEEAGEFSPNVPKSLSSAVKVKIGTSLEWGGTSEPKKFDD SVILRPSKSVKLRSPKSELHQDRSSPPPPLPERTLESFFLADEDCMQAQSIETYSTSYPDTMENSTSSKQTLKTPGKSFTRSKSLKILRN

Protein Functional Features

Main function of this protein. (from UniProt)

PTPN22 (go to UniProt):Q9Y2R2

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
Q9Y2R2	Domain	24	289	Note=Tyrosine-protein phosphatase;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00160	Type=Deletion;Start=251;End=305
Q9Y2R2	Domain	24	289	Note=Tyrosine-protein phosphatase;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00160	Type=Deletion;Start=137;End=160
Q9Y2R2	Domain	24	289	Note=Tyrosine-protein phosphatase;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00160	Type=Substitution;Start=181;End=203
Q9Y2R2	Domain	24	289	Note=Tyrosine-protein phosphatase;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00160	Type=Deletion;Start=204;End=807
Q9Y2R2	Domain	24	289	Note=Tyrosine-protein phosphatase;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00160	Type=Deletion;Start=124;End=250
Q9Y2R2	Region	676	700	Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Substitution;Start=685;End=807
Q9Y2R2	Region	676	700	Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Deletion;Start=204;End=807
Q9Y2R2	Region	724	746	Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Substitution;Start=685;End=807
Q9Y2R2	Region	724	746	Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Deletion;Start=204;End=807

Gene Isoform Structures and Expression Levels for PTPN22

Gene structures of our canonical and alternative spliced genes of PTPN22
* 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 Q9Y2R2-1

3D view using mol* of Q9Y2R2-2

3D view using mol* of Q9Y2R2-3

3D view using mol* of Q9Y2R2-4

3D view using mol* of Q9Y2R2-5

3D view using mol* of Q9Y2R2-6

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 Q9Y2R2-1

pLDDT distribution across the protein length of Q9Y2R2-2

pLDDT distribution across the protein length of Q9Y2R2-3

pLDDT distribution across the protein length of Q9Y2R2-4

pLDDT distribution across the protein length of Q9Y2R2-5

pLDDT distribution across the protein length of Q9Y2R2-6

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 Q9Y2R2-1

Ramachandran plot of Q9Y2R2-2

Ramachandran plot of Q9Y2R2-6

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
Q9Y2R2-1	1.044	231	1.076	579.327	0.517	0.733	0.967	0.849	0.933	0.91	0.617	3,94,203,206,207,209,210,213,214,217,218,219,244,2 45,247,248,249,250,289,292,293,295,296,297,300,412 ,413,414,415,416,417,418,420,421
Q9Y2R2-2	1.021	227	1.03	504.896	0.488	0.73	0.977	0.736	1.069	0.689	0.897	68,69,89,90,91,92,93,94,95,96,242,246,251,253,256, 257,259,260,261,263,264,265,267,268,444,446,447,44 9,450,451,452,455
Q9Y2R2-3	1.017	618	1.053	1819.615	0.548	0.691	0.902	0.68	0.926	0.734	0.852	1,6,9,10,13,14,17,18,19,23,26,27,28,30,31,32,34,35 ,38,39,42,44,45,46,47,50,55,56,58,59,60,61,62,63,6 4,65,66,68,69,86,87,88,89,90,91,92,96,97,99,101,10 2,103,106,107,108,132,136,137,138,140,193,194,195, 196,197,198,199,202,205,227,228,229,230,231,232,23 3,234,235,236,238,239,240,242,321,322,323,324,325, 326,327,328,329,330,565,568,569,570,571,572,573,57 5
Q9Y2R2-4	1.01	107	1.03	440.412	0.614	0.71	0.986	0.432	1.031	0.419	1.174	68,69,89,90,91,92,93,94,96,97,242,246,251,253,254, 255,256,257,261,264,265,268,446,449,450,451,452,45 3
Q9Y2R2-5	1.05	135	1.114	352.947	0.547	0.679	0.881	1.211	0.715	1.694	0.618	59,98,99,100,101,102,103,104,105,110,113,114,116,1 17,122,123,124,125,126,127,128,129,148,150,164
Q9Y2R2-6	1.029	325	1.087	1155.91	0.66	0.664	0.812	0.776	0.771	1.007	1.157	29,32,33,35,36,38,39,42,44,45,46,47,49,50,55,58,60 ,61,62,63,64,65,66,68,69,86,87,88,89,90,91,96,97,1 01,102,103,113,114,117,122,124,125,129,134,135,138 ,142,143,144,145,146,147,151,154,155,158,159,162,1 63,166,167,170,481,482,484,485,487,488,489,490,491 ,657,659,660,661,662,663,664,665

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 Q9Y2R2-1_Q9Y2R2-1_4j51_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 Q9Y2R2-1_4j51_A_Q9Y2R2-2.pdb

3D view using mol* of Q9Y2R2-1_4j51_A_Q9Y2R2-3.pdb

3D view using mol* of Q9Y2R2-1_4j51_A_Q9Y2R2-4.pdb

3D view using mol* of Q9Y2R2-1_4j51_A_Q9Y2R2-5.pdb

3D view using mol* of Q9Y2R2-1_4j51_A_Q9Y2R2-6.pdb

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

3D view using mol* of Q9Y2R2-1_Q9Y2R2-2.pdb

3D view using mol* of Q9Y2R2-1_Q9Y2R2-3.pdb

3D view using mol* of Q9Y2R2-1_Q9Y2R2-4.pdb

3D view using mol* of Q9Y2R2-1_Q9Y2R2-5.pdb

3D view using mol* of Q9Y2R2-1_Q9Y2R2-6.pdb

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

./stats/secondary_structure/figure/Q9Y2R2-1_vs_Q9Y2R2-2.png