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:CD55

Protein Summary

Gene summary

Gene name: CD55
ASpdb.0 ID: 1604
	Gene
Gene symbol	CD55
Gene ID	1604
Gene name	CD55 molecule (Cromer blood group)
Synonyms	CHAPLE\|CR\|CROM\|DAF\|TC
Cytomap	1q32.2
Type of gene	protein-coding
Description	complement decay-accelerating factorCD55 antigenCD55 molecule, decay accelerating factor for complement (Cromer blood group)Cromer blood group antigenRh blood group D antigen
Modification date	20240403
UniProtAcc	P08174

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

Partner	Gene	GO ID	GO term	PubMed ID
Gene	CD55	GO:0001618	virus receptor activity	7525274
Gene	CD55	GO:0002726	positive regulation of T cell cytokine production	16818763
Gene	CD55	GO:0005886	plasma membrane	6211481
Gene	CD55	GO:0007204	positive regulation of cytosolic calcium ion concentration	8223854
Gene	CD55	GO:0008289	lipid binding	12731067
Gene	CD55	GO:0009986	cell surface	15907827
Gene	CD55	GO:0030449	regulation of complement activation	25284781
Gene	CD55	GO:0031664	regulation of lipopolysaccharide-mediated signaling pathway	12731067
Gene	CD55	GO:0045121	membrane raft	11313396
Gene	CD55	GO:0045916	negative regulation of complement activation	6211481
Gene	CD55	GO:1903659	regulation of complement-dependent cytotoxicity	25284781
Gene	CD55	GO:2000516	positive regulation of CD4-positive, alpha-beta T cell activation	16818763
Gene	CD55	GO:2000563	positive regulation of CD4-positive, alpha-beta T cell proliferation	16818763

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
P08174-1	P08174-1_3iyp_F.pdb	3IYP	EM		F	34	285

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

P08174

CD55

P08174-1

P08174-2

381

440

362

381

Substitution

HTCFTLTGLLGTLVTMGLLT

SRPVTQAGMRWCDRSSLQSRTPGFKRSFHFSLPSSWYYRAHVFHVDRFAWDASNHGLADLAKEELRRKYTQVYRLFLVS

362

440

P08174

CD55

P08174-1

P08174-3

381

384

361

381

Substitution

GHTCFTLTGLLGTLVTMGLLT

ALQVRPFEVSGSSHISSKKMMCIL

361

384

P08174

CD55

P08174-1

P08174-4

381

364

361

381

Substitution

GHTCFTLTGLLGTLVTMGLLT

VLFM

361

364

P08174

CD55

P08174-1

P08174-5

381

439

361

381

Substitution

GHTCFTLTGLLGTLVTMGLLT

ETVFHRVIQDGLDLLASRSACLGLPKCWDYRREPPHLARAHVFHVDRFAWDASNHGLADLAKEELRRKYTQVYRLFLVS

361

439

P08174

CD55

P08174-1

P08174-6

381

525

327

Substitution

GTETPSVLQKHTTENVSATRTPPTPQKPTTVNVPATIVTPTPQKPTTINVPATGVSSTPQRHTIVNVSATGTLPTLQKPTRANDSATKSPAAAQTSFISKTLSTKTPSAAQNPMMTNASATQATLTAQKFTTAKVAFTQSPSAAP

327

471

P08174

CD55

P08174-1

P08174-7

381

551

326

Substitution

QGTETPSVLQKHTTENVSATRTPPTPQKPTTVNVPATIVTPTPQKPTTINVPATGVSSTPQRHTIVNVSATGTLPTLQKPTRANDSATKSPAAAQTSFISKTLSTKTPSAAQNPMMTNASATQATLTAQKFTTAKVAFTQSPSAARKSTNVHSPVTNGLKSTQRFPSAHIT

326

496

Multiple sequence alignment of our canonical and alternatively spliced CD55

Matched gene isoform IDs with Ensembl and RefSeq of our canonical and alternative spliced genes of CD55

UniProt-id	ENSG	ENST	ENSP
P08174-1	ENSG00000196352.18	ENST00000367064.9	ENSP00000356031.4
P08174-2	ENSG00000196352.18	ENST00000314754.12	ENSP00000316333.8
P08174-3	ENSG00000196352.18	ENST00000644836.1	ENSP00000495518.1
P08174-5	ENSG00000196352.18	ENST00000645323.1	ENSP00000496251.1

UniProt-id	NM ID	NP ID
P08174-1	NM_000574.4	NP_000565.1
P08174-2	NM_001114752.2	NP_001108224.1
P08174-3	NM_001300904.1	NP_001287833.1
P08174-5	NM_001300903.1	NP_001287832.1

Amino acid sequences of our canonical and alternatively spliced CD55

accession_id	Protein sequence
P08174-1	MTVARPSVPAALPLLGELPRLLLLVLLCLPAVWGDCGLPPDVPNAQPALEGRTSFPEDTVITYKCEESFVKIPGEKDSVICLKGSQWSDI EEFCNRSCEVPTRLNSASLKQPYITQNYFPVGTVVEYECRPGYRREPSLSPKLTCLQNLKWSTAVEFCKKKSCPNPGEIRNGQIDVPGGI LFGATISFSCNTGYKLFGSTSSFCLISGSSVQWSDPLPECREIYCPAPPQIDNGIIQGERDHYGYRQSVTYACNKGFTMIGEHSIYCTVN NDEGEWSGPPPECRGKSLTSKVPPTVQKPTTVNVPTTEVSPTSQKTTTKTTTPNAQATRSTPVSRTTKHFHETTPNKGSGTTSGTTRLLS
P08174-2	MTVARPSVPAALPLLGELPRLLLLVLLCLPAVWGDCGLPPDVPNAQPALEGRTSFPEDTVITYKCEESFVKIPGEKDSVICLKGSQWSDI EEFCNRSCEVPTRLNSASLKQPYITQNYFPVGTVVEYECRPGYRREPSLSPKLTCLQNLKWSTAVEFCKKKSCPNPGEIRNGQIDVPGGI LFGATISFSCNTGYKLFGSTSSFCLISGSSVQWSDPLPECREIYCPAPPQIDNGIIQGERDHYGYRQSVTYACNKGFTMIGEHSIYCTVN NDEGEWSGPPPECRGKSLTSKVPPTVQKPTTVNVPTTEVSPTSQKTTTKTTTPNAQATRSTPVSRTTKHFHETTPNKGSGTTSGTTRLLS
P08174-3	MTVARPSVPAALPLLGELPRLLLLVLLCLPAVWGDCGLPPDVPNAQPALEGRTSFPEDTVITYKCEESFVKIPGEKDSVICLKGSQWSDI EEFCNRSCEVPTRLNSASLKQPYITQNYFPVGTVVEYECRPGYRREPSLSPKLTCLQNLKWSTAVEFCKKKSCPNPGEIRNGQIDVPGGI LFGATISFSCNTGYKLFGSTSSFCLISGSSVQWSDPLPECREIYCPAPPQIDNGIIQGERDHYGYRQSVTYACNKGFTMIGEHSIYCTVN NDEGEWSGPPPECRGKSLTSKVPPTVQKPTTVNVPTTEVSPTSQKTTTKTTTPNAQATRSTPVSRTTKHFHETTPNKGSGTTSGTTRLLS
P08174-4	MTVARPSVPAALPLLGELPRLLLLVLLCLPAVWGDCGLPPDVPNAQPALEGRTSFPEDTVITYKCEESFVKIPGEKDSVICLKGSQWSDI EEFCNRSCEVPTRLNSASLKQPYITQNYFPVGTVVEYECRPGYRREPSLSPKLTCLQNLKWSTAVEFCKKKSCPNPGEIRNGQIDVPGGI LFGATISFSCNTGYKLFGSTSSFCLISGSSVQWSDPLPECREIYCPAPPQIDNGIIQGERDHYGYRQSVTYACNKGFTMIGEHSIYCTVN NDEGEWSGPPPECRGKSLTSKVPPTVQKPTTVNVPTTEVSPTSQKTTTKTTTPNAQATRSTPVSRTTKHFHETTPNKGSGTTSGTTRLLS
P08174-5	MTVARPSVPAALPLLGELPRLLLLVLLCLPAVWGDCGLPPDVPNAQPALEGRTSFPEDTVITYKCEESFVKIPGEKDSVICLKGSQWSDI EEFCNRSCEVPTRLNSASLKQPYITQNYFPVGTVVEYECRPGYRREPSLSPKLTCLQNLKWSTAVEFCKKKSCPNPGEIRNGQIDVPGGI LFGATISFSCNTGYKLFGSTSSFCLISGSSVQWSDPLPECREIYCPAPPQIDNGIIQGERDHYGYRQSVTYACNKGFTMIGEHSIYCTVN NDEGEWSGPPPECRGKSLTSKVPPTVQKPTTVNVPTTEVSPTSQKTTTKTTTPNAQATRSTPVSRTTKHFHETTPNKGSGTTSGTTRLLS
P08174-6	MTVARPSVPAALPLLGELPRLLLLVLLCLPAVWGDCGLPPDVPNAQPALEGRTSFPEDTVITYKCEESFVKIPGEKDSVICLKGSQWSDI EEFCNRSCEVPTRLNSASLKQPYITQNYFPVGTVVEYECRPGYRREPSLSPKLTCLQNLKWSTAVEFCKKKSCPNPGEIRNGQIDVPGGI LFGATISFSCNTGYKLFGSTSSFCLISGSSVQWSDPLPECREIYCPAPPQIDNGIIQGERDHYGYRQSVTYACNKGFTMIGEHSIYCTVN NDEGEWSGPPPECRGKSLTSKVPPTVQKPTTVNVPTTEVSPTSQKTTTKTTTPNAQGTETPSVLQKHTTENVSATRTPPTPQKPTTVNVP ATIVTPTPQKPTTINVPATGVSSTPQRHTIVNVSATGTLPTLQKPTRANDSATKSPAAAQTSFISKTLSTKTPSAAQNPMMTNASATQAT
P08174-7	MTVARPSVPAALPLLGELPRLLLLVLLCLPAVWGDCGLPPDVPNAQPALEGRTSFPEDTVITYKCEESFVKIPGEKDSVICLKGSQWSDI EEFCNRSCEVPTRLNSASLKQPYITQNYFPVGTVVEYECRPGYRREPSLSPKLTCLQNLKWSTAVEFCKKKSCPNPGEIRNGQIDVPGGI LFGATISFSCNTGYKLFGSTSSFCLISGSSVQWSDPLPECREIYCPAPPQIDNGIIQGERDHYGYRQSVTYACNKGFTMIGEHSIYCTVN NDEGEWSGPPPECRGKSLTSKVPPTVQKPTTVNVPTTEVSPTSQKTTTKTTTPNAQGTETPSVLQKHTTENVSATRTPPTPQKPTTVNVP ATIVTPTPQKPTTINVPATGVSSTPQRHTIVNVSATGTLPTLQKPTRANDSATKSPAAAQTSFISKTLSTKTPSAAQNPMMTNASATQAT LTAQKFTTAKVAFTQSPSAARKSTNVHSPVTNGLKSTQRFPSAHITATRSTPVSRTTKHFHETTPNKGSGTTSGTTRLLSGHTCFTLTGL

Protein Functional Features

Main function of this protein. (from UniProt)

CD55 (go to UniProt):P08174

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
P08174	Region	277	354	Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Substitution;Start=327;End=327
P08174	Region	277	354	Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Substitution;Start=326;End=326
P08174	Compositional bias	290	354	Note=Polar residues;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Substitution;Start=327;End=327
P08174	Compositional bias	290	354	Note=Polar residues;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Substitution;Start=326;End=326

Gene Isoform Structures and Expression Levels for CD55

Gene structures of our canonical and alternative spliced genes of CD55
* 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 P08174-1

3D view using mol* of P08174-2

3D view using mol* of P08174-3

3D view using mol* of P08174-4

3D view using mol* of P08174-5

3D view using mol* of P08174-6

3D view using mol* of P08174-7

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 P08174-1

pLDDT distribution across the protein length of P08174-2

pLDDT distribution across the protein length of P08174-3

pLDDT distribution across the protein length of P08174-4

pLDDT distribution across the protein length of P08174-5

pLDDT distribution across the protein length of P08174-6

pLDDT distribution across the protein length of P08174-7

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 P08174-1

Ramachandran plot of P08174-3

Ramachandran plot of P08174-4

Ramachandran plot of P08174-6

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
P08174-1	0.594	32	0.545	67.914	0.733	0.543	0.756	0.149	0.959	0.155	1.496	66,67,68,69,70,97,98,99,100,117,119,149,150
P08174-2	1.024	145	1.096	400.624	0.615	0.629	0.786	0.907	0.679	1.335	0.737	103,104,105,130,131,133,182,183,199,201,203,204,20 5,206,214,215,396,397,400,401,404,407,408,411,412
P08174-3	0.659	34	0.43	62.769	0.558	0.645	1.025	0.109	1.55	0.071	1.216	100,101,102,103,108,109,113,114,127,130
P08174-4	0.541	20	0.354	68.6	0.683	0.618	0.899	0.14	1.342	0.104	0.83	100,101,102,103,104,107,108,109,114,127,130
P08174-5	1.088	198	1.179	873.964	0.618	0.678	0.87	1.399	0.515	2.718	0.83	103,105,130,131,133,182,183,203,205,206,359,361,36 3,364,365,367,368,371,372,374,375,401,402,403,404, 405,406,407,408,409,410,411,412,417,420,421,424,42 5,428,429,432,435,436
P08174-6	0.675	47	0.648	119.021	0.776	0.539	0.703	0.199	0.982	0.203	1.058	65,66,67,68,69,70,96,97,98,99,101,102,104,127,143, 149,150,151,152,153,154
P08174-7	0.61	36	0.561	92.61	0.758	0.545	0.751	0.243	1.013	0.24	1.188	65,66,67,68,69,70,97,98,99,149,150,151

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 P08174-1_P08174-1_3iyp_F.pdb

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

3D view using mol* of P08174-1_3iyp_F_P08174-2.pdb

3D view using mol* of P08174-1_3iyp_F_P08174-3.pdb

3D view using mol* of P08174-1_3iyp_F_P08174-4.pdb

3D view using mol* of P08174-1_3iyp_F_P08174-5.pdb

3D view using mol* of P08174-1_3iyp_F_P08174-6.pdb

3D view using mol* of P08174-1_3iyp_F_P08174-7.pdb

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

3D view using mol* of P08174-1_P08174-2.pdb

3D view using mol* of P08174-1_P08174-3.pdb

3D view using mol* of P08174-1_P08174-4.pdb

3D view using mol* of P08174-1_P08174-5.pdb

3D view using mol* of P08174-1_P08174-6.pdb

3D view using mol* of P08174-1_P08174-7.pdb

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

./stats/secondary_structure/figure/P08174-1_vs_P08174-2.png

./stats/secondary_structure/figure/P08174-1_vs_P08174-3.png

./stats/secondary_structure/figure/P08174-1_vs_P08174-4.png

./stats/secondary_structure/figure/P08174-1_vs_P08174-5.png

./stats/secondary_structure/figure/P08174-1_vs_P08174-6.png

./stats/secondary_structure/figure/P08174-1_vs_P08174-7.png

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

./stats/relative_asa/P08174-1_vs_P08174-2.png

./stats/relative_asa/P08174-1_vs_P08174-3.png

./stats/relative_asa/P08174-1_vs_P08174-4.png

./stats/relative_asa/P08174-1_vs_P08174-5.png

./stats/relative_asa/P08174-1_vs_P08174-6.png

./stats/relative_asa/P08174-1_vs_P08174-7.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 CD55

Drugs targeting this gene/protein.
(DrugBank)

UniProt accession	Gene name	DrugBank ID	Drug name	Drug group	Actions
P08174	CD55	DB00446	Chloramphenicol	approved, vet_approved, withdrawn	other

Related Diseases to CD55

Previous studies relating to the alternative splicing of CD55 and disease information from the MeSH term (PubMed)

Gene

PMID

Title

Abstract

MeSH ID

MeSH term

Clinically important variants in CD55

(ClinVar, 04/20/2024)

accession_id

uniprot_id

gene_name

Type

Variant

Clinical_significance