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:CASP7

Protein Summary

Gene summary

Gene name: CASP7
ASpdb.0 ID: 840
	Gene
Gene symbol	CASP7
Gene ID	840
Gene name	caspase 7
Synonyms	CASP-7\|CMH-1\|ICE-LAP3\|LICE2\|MCH3
Cytomap	10q25.3
Type of gene	protein-coding
Description	caspase-7ICE-like apoptotic protease 3apoptotic protease MCH-3caspase 7, apoptosis-related cysteine peptidasecaspase 7, apoptosis-related cysteine protease
Modification date	20240407
UniProtAcc	P55210

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

Partner	Gene	GO ID	GO term	PubMed ID
Gene	CASP7	GO:0003723	RNA binding	31586028
Gene	CASP7	GO:0004197	cysteine-type endopeptidase activity	17646170\|19617626\|21157428\|22464733\|23650375\|23897474\|24904167\|27032039\|31586028\|37327784
Gene	CASP7	GO:0005634	nucleus	16374543\|19617626\|21555521\|22464733
Gene	CASP7	GO:0005634	nucleus	17167422
Gene	CASP7	GO:0005737	cytoplasm	21555521
Gene	CASP7	GO:0005829	cytosol	16352606
Gene	CASP7	GO:0005829	cytosol	17167422
Gene	CASP7	GO:0006508	proteolysis	12888622
Gene	CASP7	GO:0006915	apoptotic process	17464193
Gene	CASP7	GO:0008233	peptidase activity	19740745
Gene	CASP7	GO:0030163	protein catabolic process	16374543\|22184066\|22464733
Gene	CASP7	GO:0051604	protein maturation	21157428
Gene	CASP7	GO:0071222	cellular response to lipopolysaccharide	22464733
Gene	CASP7	GO:0097153	cysteine-type endopeptidase activity involved in apoptotic process	11257230\|19581639
Gene	CASP7	GO:0097194	execution phase of apoptosis	16374543\|16916640\|22184066\|31586028
Gene	CASP7	GO:0097200	cysteine-type endopeptidase activity involved in execution phase of apoptosis	16123041\|16352606\|16374543\|16916640\|18723680\|20566630\|22184066\|22451931\|27889207\|28863261

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
P55210-1	P55210-1_1gqf_A.pdb	1GQF	X-ray	2.9	A	47	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

P55210

CASP7

P55210-1

P55210-2

303

253

149

303

Substitution

VIYGKDGVTPIKDLTAHFRGDRCKTLLEKPKLFFIQACRGTELDDGIQADSGPINDTDANPRYKIPVEADFLFAYSTVPGYYSWRSPGRGSWFVQALCSILEEHGKDLEIMQILTRVNDRVARHFESQSDDPHFHEKKQIPCVVSMLTKELYFSQ

MESCSVTQAGVQRRDLGRLQPPPPRLAEGPSLMMASRPTRGPSMTQMLILDTRSQWKLTSSSPIPRFQAITRGGAQEEAPGLCKPSAPSWRSTEKTWKSCRSSPG

149

253

P55210

CASP7

P55210-1

P55210-3

303

336

Substitution

MDCVGWPPGRKWHLEKNTSCGGSSGICASYVTQM

P55210

CASP7

P55210-1

P55210-4

303

278

Substitution

MADDQGCIEEQGVEDSANEDSVDAKPDRSSFVPSLF

MQRGLFSDGDT

Multiple sequence alignment of our canonical and alternatively spliced CASP7

Matched gene isoform IDs with Ensembl and RefSeq of our canonical and alternative spliced genes of CASP7

UniProt-id	ENSG	ENST	ENSP
P55210-1	ENSG00000165806.21	ENST00000345633.8	ENSP00000298701.7
P55210-1	ENSG00000165806.21	ENST00000369315.5	ENSP00000358321.1
P55210-1	ENSG00000165806.21	ENST00000369318.8	ENSP00000358324.4
P55210-1	ENSG00000165806.21	ENST00000621345.4	ENSP00000480584.1
P55210-2	ENSG00000165806.21	ENST00000369331.8	ENSP00000358337.3
P55210-2	ENSG00000165806.21	ENST00000614447.4	ENSP00000478285.1
P55210-3	ENSG00000165806.21	ENST00000621607.4	ENSP00000478999.1
P55210-4	ENSG00000165806.21	ENST00000452490.3	ENSP00000398107.2

UniProt-id	NM ID	NP ID
P55210-1	NM_001227.4	NP_001218.1
P55210-1	NM_001267056.1	NP_001253985.1
P55210-1	NM_033339.4	NP_203125.1
P55210-2	NM_033340.3	NP_203126.1
P55210-3	NM_033338.5	NP_203124.1
P55210-4	NM_001267058.1	NP_001253987.1

Amino acid sequences of our canonical and alternatively spliced CASP7

accession_id	Protein sequence
P55210-1	MADDQGCIEEQGVEDSANEDSVDAKPDRSSFVPSLFSKKKKNVTMRSIKTTRDRVPTYQYNMNFEKLGKCIIINNKNFDKVTGMGVRNGT DKDAEALFKCFRSLGFDVIVYNDCSCAKMQDLLKKASEEDHTNAACFACILLSHGEENVIYGKDGVTPIKDLTAHFRGDRCKTLLEKPKL FFIQACRGTELDDGIQADSGPINDTDANPRYKIPVEADFLFAYSTVPGYYSWRSPGRGSWFVQALCSILEEHGKDLEIMQILTRVNDRVA
P55210-2	MADDQGCIEEQGVEDSANEDSVDAKPDRSSFVPSLFSKKKKNVTMRSIKTTRDRVPTYQYNMNFEKLGKCIIINNKNFDKVTGMGVRNGT DKDAEALFKCFRSLGFDVIVYNDCSCAKMQDLLKKASEEDHTNAACFACILLSHGEENMESCSVTQAGVQRRDLGRLQPPPPRLAEGPSL
P55210-3	MDCVGWPPGRKWHLEKNTSCGGSSGICASYVTQMADDQGCIEEQGVEDSANEDSVDAKPDRSSFVPSLFSKKKKNVTMRSIKTTRDRVPT YQYNMNFEKLGKCIIINNKNFDKVTGMGVRNGTDKDAEALFKCFRSLGFDVIVYNDCSCAKMQDLLKKASEEDHTNAACFACILLSHGEE NVIYGKDGVTPIKDLTAHFRGDRCKTLLEKPKLFFIQACRGTELDDGIQADSGPINDTDANPRYKIPVEADFLFAYSTVPGYYSWRSPGR
P55210-4	MQRGLFSDGDTSKKKKNVTMRSIKTTRDRVPTYQYNMNFEKLGKCIIINNKNFDKVTGMGVRNGTDKDAEALFKCFRSLGFDVIVYNDCS CAKMQDLLKKASEEDHTNAACFACILLSHGEENVIYGKDGVTPIKDLTAHFRGDRCKTLLEKPKLFFIQACRGTELDDGIQADSGPINDT DANPRYKIPVEADFLFAYSTVPGYYSWRSPGRGSWFVQALCSILEEHGKDLEIMQILTRVNDRVARHFESQSDDPHFHEKKQIPCVVSML

Protein Functional Features

Main function of this protein. (from UniProt)

CASP7 (go to UniProt):P55210

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
P55210	Region	1	30	Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Substitution;Start=1;End=1
P55210	Region	1	30	Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Substitution;Start=1;End=36
P55210	Region	187	196	Note=Loop L2;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:23897474;Dbxref=PMID:23897474	Type=Substitution;Start=149;End=303
P55210	Region	226	238	Note=Loop L3;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:23897474;Dbxref=PMID:23897474	Type=Substitution;Start=149;End=303
P55210	Region	274	288	Note=Loop L4;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:23897474;Dbxref=PMID:23897474	Type=Substitution;Start=149;End=303
P55210	Compositional bias	1	17	Note=Acidic residues;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Substitution;Start=1;End=1
P55210	Compositional bias	1	17	Note=Acidic residues;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Substitution;Start=1;End=36

Gene Isoform Structures and Expression Levels for CASP7

Gene structures of our canonical and alternative spliced genes of CASP7
* 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 P55210-1

3D view using mol* of P55210-2

3D view using mol* of P55210-3

3D view using mol* of P55210-4

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 P55210-1

pLDDT distribution across the protein length of P55210-2

pLDDT distribution across the protein length of P55210-3

pLDDT distribution across the protein length of P55210-4

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 P55210-1

Ramachandran plot of P55210-2

Ramachandran plot of P55210-3

Ramachandran plot of P55210-4

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
P55210-1	0.639	24	0.555	130.683	0.733	0.711	0.896	0.222	1.019	0.218	1.46	148,159,160,163,187,216,221,223,294
P55210-2	1.003	247	1.044	820.113	0.604	0.66	0.867	0.672	0.896	0.75	1.149	75,77,78,79,82,113,114,115,116,117,119,120,123,124 ,126,127,137,141,143,145,146,147,148,149,150,151,1 52,153,154,157,159,160,161,162,164,183,184,186,187 ,188,189,190,191,192,193,194,198,204
P55210-3	0.818	58	0.827	206.829	0.68	0.616	0.882	0.89	0.792	1.124	0.655	32,33,34,35,36,107,124,127,128,131,135,139,140,141 ,142,143,144,145
P55210-4	0.973	110	0.97	271.656	0.611	0.658	0.881	0.375	1.119	0.335	0.376	59,62,118,119,120,121,159,160,161,163,164,205,206, 207,208,209,210,212,215,247,248,249,250,251,252,25 7

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 P55210-1_P55210-1_1gqf_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 P55210-1_1gqf_A_P55210-2.pdb

3D view using mol* of P55210-1_1gqf_A_P55210-3.pdb

3D view using mol* of P55210-1_1gqf_A_P55210-4.pdb

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

3D view using mol* of P55210-1_P55210-2.pdb

3D view using mol* of P55210-1_P55210-3.pdb

3D view using mol* of P55210-1_P55210-4.pdb

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

./stats/secondary_structure/figure/P55210-1_vs_P55210-2.png

./stats/secondary_structure/figure/P55210-1_vs_P55210-3.png

./stats/secondary_structure/figure/P55210-1_vs_P55210-4.png

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

./stats/relative_asa/P55210-1_vs_P55210-2.png

./stats/relative_asa/P55210-1_vs_P55210-3.png

./stats/relative_asa/P55210-1_vs_P55210-4.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 CASP7

Drugs targeting this gene/protein.
(DrugBank)

UniProt accession	Gene name	DrugBank ID	Drug name	Drug group	Actions
P55210	CASP7	DB05408	Emricasan	investigational
P55210	CASP7	DB06255	Incadronic acid	experimental	activator
P55210	CASP7	DB03384	Fica	experimental

Related Diseases to CASP7

Previous studies relating to the alternative splicing of CASP7 and disease information from the MeSH term (PubMed)

Gene

PMID

Title

Abstract

MeSH ID

MeSH term

Clinically important variants in CASP7

(ClinVar, 04/20/2024)

accession_id

uniprot_id

gene_name

Type

Variant

Clinical_significance