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:PRSS3

Protein Summary

Gene summary

Gene name: PRSS3
ASpdb.0 ID: 5646
	Gene
Gene symbol	PRSS3
Gene ID	5646
Gene name	serine protease 3
Synonyms	MTG\|PRSS4\|T9\|TRY3\|TRY4
Cytomap	9p13.3
Type of gene	protein-coding
Description	trypsin-3brain trypsinogenmesotrypsinmesotrypsinogenpancreatic trypsinogen IIIprotease, serine 3protease, serine, 4 (trypsin 4, brain)trypsin IIItrypsin IVtrypsinogen 4trypsinogen 5trypsinogen IV
Modification date	20240407
UniProtAcc	P35030

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

Partner	Gene	GO ID	GO term	PubMed ID
Gene	PRSS3	GO:0004252	serine-type endopeptidase activity	6698368\|11827488\|14507909\|25301953
Gene	PRSS3	GO:0005509	calcium ion binding	6698368\|11827488
Gene	PRSS3	GO:0005615	extracellular space	6698368
Gene	PRSS3	GO:0006508	proteolysis	6698368\|11827488
Gene	PRSS3	GO:0031638	zymogen activation	6698368

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
P35030-1	P35030-1_5tp0_A.pdb	5TP0	X-ray	1.25	A	81	304

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

P35030

PRSS3

P35030-1

P35030-2

304

260

Substitution

MCGPDDRCPARWPGPGRAVKCGKGLAAARPGRVERGGAQRGGAGL

P35030

PRSS3

P35030-1

P35030-3

304

247

Substitution

MCGPDDRCPARWPGPGRAVKCGKGLAAARPGRVERGGAQRGGAGLELHPLLGGRTWRAARDADGCEALGT

MNPFLILAFVGAA

P35030

PRSS3

P35030-1

P35030-4

304

261

Substitution

MCGPDDRCPARWPGPGRAVKCGKGLAAARPGRVERGGAQRGGAGLELHPLLGGRTWRAARDADGCEALGTV

MHMRETSGFTLKKGRSAPLVFHPPDALI

P35030

PRSS3

P35030-1

P35030-5

304

240

Substitution

MCGPDDRCPARWPGPGRAVKCGKGLAAARPGRVERGGAQRGGAGLELHPLLGGRTWRAARDADGCEALGT

MGPAGE

Multiple sequence alignment of our canonical and alternatively spliced PRSS3

Matched gene isoform IDs with Ensembl and RefSeq of our canonical and alternative spliced genes of PRSS3

UniProt-id	ENSG	ENST	ENSP
P35030-3	ENSG00000010438.17	ENST00000379405.4	ENSP00000368715.3
P35030-5	ENSG00000010438.17	ENST00000429677.8	ENSP00000401828.3

UniProt-id	NM ID	NP ID
P35030-3	NM_002771.3	NP_002762.2
P35030-4	NM_001197097.2	NP_001184026.2

Amino acid sequences of our canonical and alternatively spliced PRSS3

accession_id	Protein sequence
P35030-1	MCGPDDRCPARWPGPGRAVKCGKGLAAARPGRVERGGAQRGGAGLELHPLLGGRTWRAARDADGCEALGTVAVPFDDDDKIVGGYTCEEN SLPYQVSLNSGSHFCGGSLISEQWVVSAAHCYKTRIQVRLGEHNIKVLEGNEQFINAAKIIRHPKYNRDTLDNDIMLIKLSSPAVINARV STISLPTTPPAAGTECLISGWGNTLSFGADYPDELKCLDAPVLTQAECKASYPGKITNSMFCVGFLEGGKDSCQRDSGGPVVCNGQLQGV
P35030-2	MELHPLLGGRTWRAARDADGCEALGTVAVPFDDDDKIVGGYTCEENSLPYQVSLNSGSHFCGGSLISEQWVVSAAHCYKTRIQVRLGEHN IKVLEGNEQFINAAKIIRHPKYNRDTLDNDIMLIKLSSPAVINARVSTISLPTTPPAAGTECLISGWGNTLSFGADYPDELKCLDAPVLT
P35030-3	MNPFLILAFVGAAVAVPFDDDDKIVGGYTCEENSLPYQVSLNSGSHFCGGSLISEQWVVSAAHCYKTRIQVRLGEHNIKVLEGNEQFINA AKIIRHPKYNRDTLDNDIMLIKLSSPAVINARVSTISLPTTPPAAGTECLISGWGNTLSFGADYPDELKCLDAPVLTQAECKASYPGKIT
P35030-4	MHMRETSGFTLKKGRSAPLVFHPPDALIAVPFDDDDKIVGGYTCEENSLPYQVSLNSGSHFCGGSLISEQWVVSAAHCYKTRIQVRLGEH NIKVLEGNEQFINAAKIIRHPKYNRDTLDNDIMLIKLSSPAVINARVSTISLPTTPPAAGTECLISGWGNTLSFGADYPDELKCLDAPVL
P35030-5	MGPAGEVAVPFDDDDKIVGGYTCEENSLPYQVSLNSGSHFCGGSLISEQWVVSAAHCYKTRIQVRLGEHNIKVLEGNEQFINAAKIIRHP KYNRDTLDNDIMLIKLSSPAVINARVSTISLPTTPPAAGTECLISGWGNTLSFGADYPDELKCLDAPVLTQAECKASYPGKITNSMFCVG

Protein Functional Features

Main function of this protein. (from UniProt)

PRSS3 (go to UniProt):P35030

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

Gene Isoform Structures and Expression Levels for PRSS3

Gene structures of our canonical and alternative spliced genes of PRSS3
* 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 P35030-1

3D view using mol* of P35030-2

3D view using mol* of P35030-3

3D view using mol* of P35030-4

3D view using mol* of P35030-5

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 P35030-1

pLDDT distribution across the protein length of P35030-2

pLDDT distribution across the protein length of P35030-3

pLDDT distribution across the protein length of P35030-4

pLDDT distribution across the protein length of P35030-5

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 P35030-1

Ramachandran plot of P35030-2

Ramachandran plot of P35030-3

Ramachandran plot of P35030-5

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
P35030-1	0.777	47	0.715	115.248	0.624	0.709	1.08	0.316	1.089	0.29	1.32	120,232,251,252,253,254,255,257,271,273,274,275,27 6,277,282,283,284,285
P35030-2	0.809	45	0.648	114.905	0.559	0.773	1.184	0.198	1.369	0.145	1.127	188,207,208,209,210,211,213,227,228,229,230,231,23 2,233,238,239,240
P35030-3	0.808	52	0.707	117.992	0.6	0.716	1.066	0.23	1.228	0.187	1.023	63,175,194,195,196,197,200,214,215,216,217,218,219 ,220,221,225,226,227
P35030-4	0.786	50	0.679	155.722	0.669	0.699	1.109	0.157	1.243	0.126	1.297	77,160,162,163,164,165,189,208,209,210,211,212,214 ,228,230,231,232,233,234,236,239,241,242
P35030-5	0.756	40	0.601	118.335	0.672	0.737	1.114	0.282	1.335	0.211	1.532	168,187,188,189,190,191,193,207,209,210,211,212,21 3,214,218,219,220,221

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 P35030-1_P35030-1_5tp0_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 P35030-1_5tp0_A_P35030-2.pdb

3D view using mol* of P35030-1_5tp0_A_P35030-3.pdb

3D view using mol* of P35030-1_5tp0_A_P35030-4.pdb

3D view using mol* of P35030-1_5tp0_A_P35030-5.pdb

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

3D view using mol* of P35030-1_P35030-2.pdb

3D view using mol* of P35030-1_P35030-3.pdb

3D view using mol* of P35030-1_P35030-4.pdb

3D view using mol* of P35030-1_P35030-5.pdb

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

./stats/secondary_structure/figure/P35030-1_vs_P35030-2.png

./stats/secondary_structure/figure/P35030-1_vs_P35030-3.png

./stats/secondary_structure/figure/P35030-1_vs_P35030-4.png

./stats/secondary_structure/figure/P35030-1_vs_P35030-5.png

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

./stats/relative_asa/P35030-1_vs_P35030-2.png

./stats/relative_asa/P35030-1_vs_P35030-3.png

./stats/relative_asa/P35030-1_vs_P35030-4.png

./stats/relative_asa/P35030-1_vs_P35030-5.png

Protein-Protein Interaction

Interactors from UniProt.

Accession_id

Subsection

Start

End

Funcitonal feature

Splicing information

Interactors from STRING.

Gene name

Interactors

Related Drugs to PRSS3

Drugs targeting this gene/protein.
(DrugBank)

UniProt accession	Gene name	DrugBank ID	Drug name	Drug group	Actions
P35030	PRSS3	DB03129	Diamino-N-[3-(1,3,2-dioxaborolan-2-yloxy)propyl]methaniminium	experimental
P35030	PRSS3	DB03127	Benzamidine	experimental
P35030	PRSS3	DB03637	Guanidine-3-propanol	experimental
P35030	PRSS3	DB04109	[4-(1,3,2-Dioxaborolan-2-Yloxy)Methyl]Benzamidine	experimental
P35030	PRSS3	DB04369	1,3,2-Dioxaborolan-2-Ol	experimental
P35030	PRSS3	DB02585	4-(Hydroxymethyl)Benzamidine	experimental
P35030	PRSS3	DB02541	4-Hydroxybutan-1-Aminium	experimental
P35030	PRSS3	DB02308	4-(1,3,2-Dioxaborolan-2-Yloxy)Butan-1-Aminium	experimental

Related Diseases to PRSS3

Previous studies relating to the alternative splicing of PRSS3 and disease information from the MeSH term (PubMed)

Gene

PMID

Title

Abstract

MeSH ID

MeSH term

Clinically important variants in PRSS3

(ClinVar, 04/20/2024)

accession_id

uniprot_id

gene_name

Type

Variant

Clinical_significance