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:PKD2

Protein Summary

Gene summary

Gene name: PKD2
ASpdb.0 ID: 5311
	Gene
Gene symbol	PKD2
Gene ID	5311
Gene name	polycystin 2, transient receptor potential cation channel
Synonyms	APKD2\|PC2\|PKD4\|Pc-2\|TRPP2
Cytomap	4q22.1
Type of gene	protein-coding
Description	polycystin-2autosomal dominant polycystic kidney disease type II proteinpolycystic kidney disease 2 (autosomal dominant)transient receptor potential cation channel subfamily P member 2
Modification date	20240411
UniProtAcc	Q13563

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

Partner	Gene	GO ID	GO term	PubMed ID
Gene	PKD2	GO:0005244	voltage-gated monoatomic ion channel activity	11854751
Gene	PKD2	GO:0005245	voltage-gated calcium channel activity	11252306\|15692563
Gene	PKD2	GO:0005248	voltage-gated sodium channel activity	11252306
Gene	PKD2	GO:0005262	calcium channel activity	27214281
Gene	PKD2	GO:0005267	potassium channel activity	26269590
Gene	PKD2	GO:0005509	calcium ion binding	24990821
Gene	PKD2	GO:0005737	cytoplasm	10770959
Gene	PKD2	GO:0005783	endoplasmic reticulum	10760273\|15123714\|15692563\|19801576\|28154160
Gene	PKD2	GO:0005789	endoplasmic reticulum membrane	11854751\|15001556
Gene	PKD2	GO:0005829	cytosol	-
Gene	PKD2	GO:0005886	plasma membrane	15692563\|16025301\|21044049\|26269590\|28092368\|29899465\|30093605
Gene	PKD2	GO:0005929	cilium	28154160
Gene	PKD2	GO:0006816	calcium ion transport	11252306\|27214281
Gene	PKD2	GO:0007166	cell surface receptor signaling pathway	27214281
Gene	PKD2	GO:0008092	cytoskeletal protein binding	10760273
Gene	PKD2	GO:0009925	basal plasma membrane	10770959
Gene	PKD2	GO:0016020	membrane	30093605
Gene	PKD2	GO:0022843	voltage-gated monoatomic cation channel activity	11252306
Gene	PKD2	GO:0030027	lamellipodium	10760273
Gene	PKD2	GO:0034703	cation channel complex	30093605
Gene	PKD2	GO:0035725	sodium ion transmembrane transport	11252306
Gene	PKD2	GO:0036064	ciliary basal body	15337773
Gene	PKD2	GO:0042803	protein homodimerization activity	9192675
Gene	PKD2	GO:0042805	actinin binding	15843396
Gene	PKD2	GO:0045180	basal cortex	10770959
Gene	PKD2	GO:0045944	positive regulation of transcription by RNA polymerase II	16311606
Gene	PKD2	GO:0048763	calcium-induced calcium release activity	11854751
Gene	PKD2	GO:0051209	release of sequestered calcium ion into cytosol	11854751
Gene	PKD2	GO:0051262	protein tetramerization	29899465
Gene	PKD2	GO:0051289	protein homotetramerization	28092368
Gene	PKD2	GO:0051290	protein heterotetramerization	30093605
Gene	PKD2	GO:0070062	extracellular exosome	37681898
Gene	PKD2	GO:0070588	calcium ion transmembrane transport	11854751
Gene	PKD2	GO:0071464	cellular response to hydrostatic pressure	16025301
Gene	PKD2	GO:0071470	cellular response to osmotic stress	16025301
Gene	PKD2	GO:0071805	potassium ion transmembrane transport	26269590
Gene	PKD2	GO:0072686	mitotic spindle	15123714
Gene	PKD2	GO:0090279	regulation of calcium ion import	11854751
Gene	PKD2	GO:0098553	lumenal side of endoplasmic reticulum membrane	21044049
Gene	PKD2	GO:0098554	cytoplasmic side of endoplasmic reticulum membrane	21044049
Gene	PKD2	GO:0140494	migrasome	37681898

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
Q13563-1	Q13563-1_5k47_A.pdb	5K47	EM	4.2	A	213	702

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

Q13563

PKD2

Q13563-1

Q13563-2

968

483

476

483

Substitution

CEIIFCFF

FICSSYGD

476

483

Q13563

PKD2

Q13563-1

Q13563-2

968

483

484

968

Deletion

none

483

Q13563

PKD2

Q13563-1

Q13563-3

968

912

517

572

Deletion

none

516

Q13563

PKD2

Q13563-1

Q13563-4

968

646

633

646

Substitution

IFTQFRIILGDINF

IICSWRSSMIRTLK

633

646

Q13563

PKD2

Q13563-1

Q13563-4

968

646

647

968

Deletion

none

646

Q13563

PKD2

Q13563-1

Q13563-5

968

874

748

841

Deletion

none

747

Multiple sequence alignment of our canonical and alternatively spliced PKD2

Matched gene isoform IDs with Ensembl and RefSeq of our canonical and alternative spliced genes of PKD2

UniProt-id	ENSG	ENST	ENSP
Q13563-1	ENSG00000118762.8	ENST00000237596.7	ENSP00000237596.2

UniProt-id	NM ID	NP ID
Q13563-1	NM_000297.3	NP_000288.1

Amino acid sequences of our canonical and alternatively spliced PKD2

accession_id	Protein sequence
Q13563-1	MVNSSRVQPQQPGDAKRPPAPRAPDPGRLMAGCAAVGASLAAPGGLCEQRGLEIEMQRIRQAAARDPPAGAAASPSPPLSSCSRQAWSRD NPGFEAEEEEEEVEGEEGGMVVEMDVEWRPGSRRSAASSAVSSVGARSRGLGGYHGAGHPSGRRRRREDQGPPCPSPVGGGDPLHRHLPL EGQPPRVAWAERLVRGLRGLWGTRLMEESSTNREKYLKSVLRELVTYLLFLIVLCILTYGMMSSNVYYYTRMMSQLFLDTPVSKTEKTNF KTLSSMEDFWKFTEGSLLDGLYWKMQPSNQTEADNRSFIFYENLLLGVPRIRQLRVRNGSCSIPQDLRDEIKECYDVYSVSSEDRAPFGP RNGTAWIYTSEKDLNGSSHWGIIATYSGAGYYLDLSRTREETAAQVASLKKNVWLDRGTRATFIDFSVYNANINLFCVVRLLVEFPATGG VIPSWQFQPLKLIRYVTTFDFFLAACEIIFCFFIFYYVVEEILEIRIHKLHYFRSFWNCLDVVIVVLSVVAIGINIYRTSNVEVLLQFLE DQNTFPNFEHLAYWQIQFNNIAAVTVFFVWIKLFKFINFNRTMSQLSTTMSRCAKDLFGFAIMFFIIFLAYAQLAYLVFGTQVDDFSTFQ ECIFTQFRIILGDINFAEIEEANRVLGPIYFTTFVFFMFFILLNMFLAIINDTYSEVKSDLAQQKAEMELSDLIRKGYHKALVKLKLKKN TVDDISESLRQGGGKLNFDELRQDLKGKGHTDAEIEAIFTKYDQDGDQELTEHEHQQMRDDLEKEREDLDLDHSSLPRPMSSRSFPRSLD DSEEDDDEDSGHSSRRRGSISSGVSYEEFQVLVRRVDRMEHSIGSIVSKIDAVIVKLEIMERAKLKRREVLGRLLDGVAEDERLGRDSEI
Q13563-2	MVNSSRVQPQQPGDAKRPPAPRAPDPGRLMAGCAAVGASLAAPGGLCEQRGLEIEMQRIRQAAARDPPAGAAASPSPPLSSCSRQAWSRD NPGFEAEEEEEEVEGEEGGMVVEMDVEWRPGSRRSAASSAVSSVGARSRGLGGYHGAGHPSGRRRRREDQGPPCPSPVGGGDPLHRHLPL EGQPPRVAWAERLVRGLRGLWGTRLMEESSTNREKYLKSVLRELVTYLLFLIVLCILTYGMMSSNVYYYTRMMSQLFLDTPVSKTEKTNF KTLSSMEDFWKFTEGSLLDGLYWKMQPSNQTEADNRSFIFYENLLLGVPRIRQLRVRNGSCSIPQDLRDEIKECYDVYSVSSEDRAPFGP RNGTAWIYTSEKDLNGSSHWGIIATYSGAGYYLDLSRTREETAAQVASLKKNVWLDRGTRATFIDFSVYNANINLFCVVRLLVEFPATGG
Q13563-3	MVNSSRVQPQQPGDAKRPPAPRAPDPGRLMAGCAAVGASLAAPGGLCEQRGLEIEMQRIRQAAARDPPAGAAASPSPPLSSCSRQAWSRD NPGFEAEEEEEEVEGEEGGMVVEMDVEWRPGSRRSAASSAVSSVGARSRGLGGYHGAGHPSGRRRRREDQGPPCPSPVGGGDPLHRHLPL EGQPPRVAWAERLVRGLRGLWGTRLMEESSTNREKYLKSVLRELVTYLLFLIVLCILTYGMMSSNVYYYTRMMSQLFLDTPVSKTEKTNF KTLSSMEDFWKFTEGSLLDGLYWKMQPSNQTEADNRSFIFYENLLLGVPRIRQLRVRNGSCSIPQDLRDEIKECYDVYSVSSEDRAPFGP RNGTAWIYTSEKDLNGSSHWGIIATYSGAGYYLDLSRTREETAAQVASLKKNVWLDRGTRATFIDFSVYNANINLFCVVRLLVEFPATGG VIPSWQFQPLKLIRYVTTFDFFLAACEIIFCFFIFYYVVEEILEIRIHKLHYFRSFWNCLDVVIVVLFKFINFNRTMSQLSTTMSRCAKD LFGFAIMFFIIFLAYAQLAYLVFGTQVDDFSTFQECIFTQFRIILGDINFAEIEEANRVLGPIYFTTFVFFMFFILLNMFLAIINDTYSE VKSDLAQQKAEMELSDLIRKGYHKALVKLKLKKNTVDDISESLRQGGGKLNFDELRQDLKGKGHTDAEIEAIFTKYDQDGDQELTEHEHQ QMRDDLEKEREDLDLDHSSLPRPMSSRSFPRSLDDSEEDDDEDSGHSSRRRGSISSGVSYEEFQVLVRRVDRMEHSIGSIVSKIDAVIVK LEIMERAKLKRREVLGRLLDGVAEDERLGRDSEIHREQMERLVREELERWESDDAASQISHGLGTPVGLNGQPRPRSSRPSSSQSTEGME
Q13563-4	MVNSSRVQPQQPGDAKRPPAPRAPDPGRLMAGCAAVGASLAAPGGLCEQRGLEIEMQRIRQAAARDPPAGAAASPSPPLSSCSRQAWSRD NPGFEAEEEEEEVEGEEGGMVVEMDVEWRPGSRRSAASSAVSSVGARSRGLGGYHGAGHPSGRRRRREDQGPPCPSPVGGGDPLHRHLPL EGQPPRVAWAERLVRGLRGLWGTRLMEESSTNREKYLKSVLRELVTYLLFLIVLCILTYGMMSSNVYYYTRMMSQLFLDTPVSKTEKTNF KTLSSMEDFWKFTEGSLLDGLYWKMQPSNQTEADNRSFIFYENLLLGVPRIRQLRVRNGSCSIPQDLRDEIKECYDVYSVSSEDRAPFGP RNGTAWIYTSEKDLNGSSHWGIIATYSGAGYYLDLSRTREETAAQVASLKKNVWLDRGTRATFIDFSVYNANINLFCVVRLLVEFPATGG VIPSWQFQPLKLIRYVTTFDFFLAACEIIFCFFIFYYVVEEILEIRIHKLHYFRSFWNCLDVVIVVLSVVAIGINIYRTSNVEVLLQFLE DQNTFPNFEHLAYWQIQFNNIAAVTVFFVWIKLFKFINFNRTMSQLSTTMSRCAKDLFGFAIMFFIIFLAYAQLAYLVFGTQVDDFSTFQ
Q13563-5	MVNSSRVQPQQPGDAKRPPAPRAPDPGRLMAGCAAVGASLAAPGGLCEQRGLEIEMQRIRQAAARDPPAGAAASPSPPLSSCSRQAWSRD NPGFEAEEEEEEVEGEEGGMVVEMDVEWRPGSRRSAASSAVSSVGARSRGLGGYHGAGHPSGRRRRREDQGPPCPSPVGGGDPLHRHLPL EGQPPRVAWAERLVRGLRGLWGTRLMEESSTNREKYLKSVLRELVTYLLFLIVLCILTYGMMSSNVYYYTRMMSQLFLDTPVSKTEKTNF KTLSSMEDFWKFTEGSLLDGLYWKMQPSNQTEADNRSFIFYENLLLGVPRIRQLRVRNGSCSIPQDLRDEIKECYDVYSVSSEDRAPFGP RNGTAWIYTSEKDLNGSSHWGIIATYSGAGYYLDLSRTREETAAQVASLKKNVWLDRGTRATFIDFSVYNANINLFCVVRLLVEFPATGG VIPSWQFQPLKLIRYVTTFDFFLAACEIIFCFFIFYYVVEEILEIRIHKLHYFRSFWNCLDVVIVVLSVVAIGINIYRTSNVEVLLQFLE DQNTFPNFEHLAYWQIQFNNIAAVTVFFVWIKLFKFINFNRTMSQLSTTMSRCAKDLFGFAIMFFIIFLAYAQLAYLVFGTQVDDFSTFQ ECIFTQFRIILGDINFAEIEEANRVLGPIYFTTFVFFMFFILLNMFLAIINDTYSEVKSDLAQQKAEMELSDLIRKGYHKALVKLKLKKN TVDDISESLRQGGGKLNFDELRQDLKGLVRRVDRMEHSIGSIVSKIDAVIVKLEIMERAKLKRREVLGRLLDGVAEDERLGRDSEIHREQ

Protein Functional Features

Main function of this protein. (from UniProt)

PKD2 (go to UniProt):Q13563

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
Q13563	Transmembrane	469	489	"Note=Helical%3B Name%3DS2;Ontology_term=ECO:0000269	ECO:0000269
Q13563	Transmembrane	469	489	"Note=Helical%3B Name%3DS2;Ontology_term=ECO:0000269	ECO:0000269
Q13563	Topological domain	490	505	"Note=Cytoplasmic;Ontology_term=ECO:0000269	ECO:0000269
Q13563	Transmembrane	506	526	"Note=Helical%3B Name%3DS3;Ontology_term=ECO:0000269	ECO:0000269
Q13563	Transmembrane	506	526	"Note=Helical%3B Name%3DS3;Ontology_term=ECO:0000269	ECO:0000269
Q13563	Topological domain	527	552	"Note=Extracellular;Ontology_term=ECO:0000269	ECO:0000269
Q13563	Topological domain	527	552	"Note=Extracellular;Ontology_term=ECO:0000269	ECO:0000269
Q13563	Transmembrane	553	573	"Note=Helical%3B Name%3DS4;Ontology_term=ECO:0000269	ECO:0000269
Q13563	Transmembrane	553	573	"Note=Helical%3B Name%3DS4;Ontology_term=ECO:0000269	ECO:0000269
Q13563	Topological domain	574	597	"Note=Cytoplasmic;Ontology_term=ECO:0000269	ECO:0000269
Q13563	Transmembrane	598	619	"Note=Helical%3B Name%3D5;Ontology_term=ECO:0000269	ECO:0000269
Q13563	Topological domain	620	631	"Note=Extracellular;Ontology_term=ECO:0000269	ECO:0000269
Q13563	Intramembrane	632	646	"Note=Pore-forming;Ontology_term=ECO:0000269	ECO:0000269
Q13563	Intramembrane	632	646	"Note=Pore-forming;Ontology_term=ECO:0000269	ECO:0000269
Q13563	Topological domain	647	654	"Note=Extracellular;Ontology_term=ECO:0000269	ECO:0000269
Q13563	Topological domain	647	654	"Note=Extracellular;Ontology_term=ECO:0000269	ECO:0000269
Q13563	Transmembrane	655	675	"Note=Helical%3B Name%3DS6;Ontology_term=ECO:0000269	ECO:0000269
Q13563	Transmembrane	655	675	"Note=Helical%3B Name%3DS6;Ontology_term=ECO:0000269	ECO:0000269
Q13563	Topological domain	676	968	"Note=Cytoplasmic;Ontology_term=ECO:0000269	ECO:0000269
Q13563	Topological domain	676	968	"Note=Cytoplasmic;Ontology_term=ECO:0000269	ECO:0000269
Q13563	Topological domain	676	968	"Note=Cytoplasmic;Ontology_term=ECO:0000269	ECO:0000269
Q13563	Domain	750	785	"Note=EF-hand;Ontology_term=ECO:0000255	ECO:0000269
Q13563	Domain	750	785	"Note=EF-hand;Ontology_term=ECO:0000255	ECO:0000269
Q13563	Domain	750	785	"Note=EF-hand;Ontology_term=ECO:0000255	ECO:0000269
Q13563	Region	764	831	Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Deletion;Start=484;End=968
Q13563	Region	764	831	Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Deletion;Start=647;End=968
Q13563	Region	764	831	Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Deletion;Start=748;End=841
Q13563	Region	803	822	Note=Linker;Ontology_term=ECO:0000305;evidence=ECO:0000305\|PubMed:18694932;Dbxref=PMID:18694932	Type=Deletion;Start=484;End=968
Q13563	Region	803	822	Note=Linker;Ontology_term=ECO:0000305;evidence=ECO:0000305\|PubMed:18694932;Dbxref=PMID:18694932	Type=Deletion;Start=647;End=968
Q13563	Region	803	822	Note=Linker;Ontology_term=ECO:0000305;evidence=ECO:0000305\|PubMed:18694932;Dbxref=PMID:18694932	Type=Deletion;Start=748;End=841
Q13563	Region	810	821	Note=Important for interaction with PACS1 and PACS2;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:15692563;Dbxref=PMID:15692563	Type=Deletion;Start=484;End=968
Q13563	Region	810	821	Note=Important for interaction with PACS1 and PACS2;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:15692563;Dbxref=PMID:15692563	Type=Deletion;Start=647;End=968
Q13563	Region	810	821	Note=Important for interaction with PACS1 and PACS2;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:15692563;Dbxref=PMID:15692563	Type=Deletion;Start=748;End=841
Q13563	Region	917	968	Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Deletion;Start=484;End=968
Q13563	Region	917	968	Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Deletion;Start=647;End=968
Q13563	Coiled coil	833	872	"Ontology_term=ECO:0000269	ECO:0000305;evidence=ECO:0000269\|PubMed:19556541
Q13563	Coiled coil	833	872	"Ontology_term=ECO:0000269	ECO:0000305;evidence=ECO:0000269\|PubMed:19556541
Q13563	Coiled coil	833	872	"Ontology_term=ECO:0000269	ECO:0000305;evidence=ECO:0000269\|PubMed:19556541
Q13563	Motif	641	643	Note=Selectivity filter;Ontology_term=ECO:0000305;evidence=ECO:0000305\|PubMed:28092368;Dbxref=PMID:28092368	Type=Deletion;Start=484;End=968
Q13563	Motif	641	643	Note=Selectivity filter;Ontology_term=ECO:0000305;evidence=ECO:0000305\|PubMed:28092368;Dbxref=PMID:28092368	Type=Substitution;Start=633;End=646
Q13563	Compositional bias	764	794	Note=Basic and acidic residues;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Deletion;Start=484;End=968
Q13563	Compositional bias	764	794	Note=Basic and acidic residues;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Deletion;Start=647;End=968
Q13563	Compositional bias	764	794	Note=Basic and acidic residues;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Deletion;Start=748;End=841
Q13563	Compositional bias	937	968	Note=Polar residues;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Deletion;Start=484;End=968
Q13563	Compositional bias	937	968	Note=Polar residues;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Deletion;Start=647;End=968

Gene Isoform Structures and Expression Levels for PKD2

Gene structures of our canonical and alternative spliced genes of PKD2
* 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 Q13563-1

3D view using mol* of Q13563-2

3D view using mol* of Q13563-3

3D view using mol* of Q13563-4

3D view using mol* of Q13563-5

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 Q13563-1

pLDDT distribution across the protein length of Q13563-2

pLDDT distribution across the protein length of Q13563-3

pLDDT distribution across the protein length of Q13563-4

pLDDT distribution across the protein length of Q13563-5

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 Q13563-1

Ramachandran plot of Q13563-2

Ramachandran plot of Q13563-4

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
Q13563-1	1.069	735	1.099	1860.089	0.451	0.767	1.006	1.141	0.922	1.236	0.982	46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62 ,64,65,234,237,238,239,240,241,242,243,245,246,247 ,250,251,254,255,258,259,271,378,379,380,381,382,3 85,433,434,435,438,440,442,454,455,456,457,458,459 ,460,461,462,464,465,469,470,473,474,477,480,481,5 17,518,521,522,525,526,528,529,532,552,553,555,556 ,557,558,559,560,561,562,563,564,565,566,624,625,6 28,630,631,634,635,637,638,641
Q13563-2	1.004	337	1.044	917.525	0.579	0.666	0.861	0.692	0.907	0.762	1.185	45,46,48,49,50,52,55,239,240,241,242,243,245,246,2 92,293,294,295,296,297,298,299,300,301,302,303,304 ,305,306,307,308,311,312,314,315,397,398,399,400,4 29,431,432,433,434,435,459,460,461,462,463,464,465 ,466,467,469,470,473,474,477
Q13563-3	1.016	110	1.036	335.797	0.565	0.716	0.954	0.653	1.022	0.638	0.693	238,239,240,241,242,243,246,316,427,433,434,435,43 6,438,459,460,461,462,464,465,466,467,469,470,473, 474
Q13563-4	1.109	256	1.16	468.538	0.503	0.78	1.009	1.818	0.763	2.385	0.978	234,237,238,239,240,241,242,243,244,245,246,433,43 4,435,458,459,460,461,462,464,465,466,467,469,470, 473,474,477,480,481,518,521,522,525,526,528,532,55 5,558,559,562,563,565,566
Q13563-5	1.188	108	1.254	173.558	0.435	0.855	1.11	3.132	0.611	5.126	0.312	234,237,238,241,242,464,477,480,481,518,521,522,52 5,526,528,558,559,562,563,565,566

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 Q13563-1_Q13563-1_5k47_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 Q13563-1_5k47_A_Q13563-2.pdb

3D view using mol* of Q13563-1_5k47_A_Q13563-3.pdb

3D view using mol* of Q13563-1_5k47_A_Q13563-4.pdb

3D view using mol* of Q13563-1_5k47_A_Q13563-5.pdb

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

3D view using mol* of Q13563-1_Q13563-2.pdb

3D view using mol* of Q13563-1_Q13563-3.pdb

3D view using mol* of Q13563-1_Q13563-4.pdb

3D view using mol* of Q13563-1_Q13563-5.pdb

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

./stats/secondary_structure/figure/Q13563-1_vs_Q13563-2.png

./stats/secondary_structure/figure/Q13563-1_vs_Q13563-3.png

./stats/secondary_structure/figure/Q13563-1_vs_Q13563-4.png

./stats/secondary_structure/figure/Q13563-1_vs_Q13563-5.png

Protein Feature Comparison of the relative accessible surface area (ASA) among the protiens.

./stats/relative_asa/Q13563-1_vs_Q13563-2.png

./stats/relative_asa/Q13563-1_vs_Q13563-3.png

./stats/relative_asa/Q13563-1_vs_Q13563-4.png

./stats/relative_asa/Q13563-1_vs_Q13563-5.png

Protein-Protein Interaction

Interactors from UniProt.

Accession_id	Subsection	Start	End	Funcitonal feature	Splicing information
Q13563	Region	810	821	Note=Important for interaction with PACS1 and PACS2;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:15692563;Dbxref=PMID:15692563	Type=Deletion;Start=484;End=968
Q13563	Region	810	821	Note=Important for interaction with PACS1 and PACS2;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:15692563;Dbxref=PMID:15692563	Type=Deletion;Start=647;End=968
Q13563	Region	810	821	Note=Important for interaction with PACS1 and PACS2;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:15692563;Dbxref=PMID:15692563	Type=Deletion;Start=748;End=841

Interactors from STRING.

Gene name

Interactors

Related Drugs to PKD2

Drugs targeting this gene/protein.
(DrugBank)

UniProt accession

Gene name

DrugBank ID

Drug name

Drug group

Actions

Related Diseases to PKD2

Previous studies relating to the alternative splicing of PKD2 and disease information from the MeSH term (PubMed)

Gene	PMID	Title	Abstract	MeSH ID	MeSH term
PKD2	12527301	Polycystin-2 associates with tropomyosin-1, an actin microfilament component.	Polycystin-2 (PC2) is the product of the second cloned gene (PKD2) responsible for autosomal dominant polycystic kidney disease and has recently been shown to be a calcium-permeable cation channel. PC2 has been shown to connect indirectly with the actin microfilament. Here, we report a direct association between PC2 and the actin microfilament. Using a yeast two-hybrid screen, we identified a specific interaction between the PC2 cytoplasmic C-terminal domain and tropomyosin-1 (TM-1), a component of the actin microfilament complex. Tropomyosins constitute a protein family of more than 20 isoforms arising mainly from alternative splicing and are present in muscle as well as non-muscle cells. We identified a new TM-1 splicing isoform in kidney and heart (TM-1a) that differs from TM-1 in the C terminus and interacted with PC2. In vitro biochemical methods, including GST pull-down, blot overlay and microtiter binding assays, confirmed the interaction between PC2 and the two TM-1 isoforms. Further experiments targeted the interacting domains to G821-R878 of PC2 and A152-E196, a common segment of TM-1 and TM-1a. Indirect double immunofluorescence experiments showed partial co-localization of PC2 and TM-1 in transfected mouse fibroblast NIH 3T3 cells. Co-immunoprecipitation (co-IP) studies using 3T3 cells and Xenopus oocytes co-expressing PC2 and TM-1 (or TM-1a) revealed in vivo association between the protein pairs. Furthermore, the in vivo interaction between the endogenous PC2 and TM-1 was demonstrated also by reciprocal co-IP using native human embryonic kidney cells and human adult kidney. Considering previous reports that TM-1 acts as a suppressor of neoplastic growth of transformed cells, it is possible that TM-1 contributes to cyst formation/growth when the anchorage of PC2 to the actin microfilament via TM-1 is altered.	D016891	Polycystic Kidney, Autosomal Dominant

Clinically important variants in PKD2

(ClinVar, 04/20/2024)

accession_id

uniprot_id

gene_name

Type

Variant

Clinical_significance