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:CD28

Protein Summary

Gene summary

Gene name: CD28
ASpdb.0 ID: 940
	Gene
Gene symbol	CD28
Gene ID	940
Gene name	CD28 molecule
Synonyms	Tp44
Cytomap	2q33.2
Type of gene	protein-coding
Description	T-cell-specific surface glycoprotein CD28
Modification date	20240305
UniProtAcc	P10747

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

Partner	Gene	GO ID	GO term	PubMed ID
Gene	CD28	GO:0005886	plasma membrane	11390434
Gene	CD28	GO:0009897	external side of plasma membrane	11390434
Gene	CD28	GO:0009986	cell surface	15067037
Gene	CD28	GO:0032733	positive regulation of interleukin-10 production	8617933
Gene	CD28	GO:0032743	positive regulation of interleukin-2 production	3875683
Gene	CD28	GO:0032753	positive regulation of interleukin-4 production	8617933
Gene	CD28	GO:0042102	positive regulation of T cell proliferation	3159820\|8617933
Gene	CD28	GO:0042110	T cell activation	23918985
Gene	CD28	GO:0045066	regulatory T cell differentiation	18641304
Gene	CD28	GO:0045840	positive regulation of mitotic nuclear division	3159820
Gene	CD28	GO:0098636	protein complex involved in cell adhesion	7544393

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
P10747-1	P10747-1_6o8d_C.pdb	6O8D	X-ray	3.55	C	20	134

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
P10747	CD28	P10747-1	P10747-2	220	101	19	137	Deletion	none	none	18	18
P10747	CD28	P10747-1	P10747-3	220	136	40	124	Substitution	CKYSYNLFSREFRASLHKGLDSAVEVCVVYGNYSQQLQVYSKTGFNCDGKLGNESVTFYLQNLYVNQTDIYFCKIEVMYPPPYLD	Y	40	40
P10747	CD28	P10747-1	P10747-4	220	123	40	137	Substitution	CKYSYNLFSREFRASLHKGLDSAVEVCVVYGNYSQQLQVYSKTGFNCDGKLGNESVTFYLQNLYVNQTDIYFCKIEVMYPPPYLDNEKSNGTIIHVKG	W	40	40
P10747	CD28	P10747-1	P10747-5	220	55	40	124	Substitution	CKYSYNLFSREFRASLHKGLDSAVEVCVVYGNYSQQLQVYSKTGFNCDGKLGNESVTFYLQNLYVNQTDIYFCKIEVMYPPPYLD	Y	40	40
P10747	CD28	P10747-1	P10747-5	220	55	138	139	Substitution	KH	EE	54	55
P10747	CD28	P10747-1	P10747-5	220	55	140	220	Deletion	none	none	55	55
P10747	CD28	P10747-1	P10747-6	220	80	40	124	Substitution	CKYSYNLFSREFRASLHKGLDSAVEVCVVYGNYSQQLQVYSKTGFNCDGKLGNESVTFYLQNLYVNQTDIYFCKIEVMYPPPYLD	Y	40	40
P10747	CD28	P10747-1	P10747-6	220	80	152	207	Deletion	none	none	67	67
P10747	CD28	P10747-1	P10747-7	220	234	1	17	Substitution	MLRLLLALNLFPSIQVT	MPCGLSALIMCPKGMVAVVVAVDDGDSQALA	1	31

Multiple sequence alignment of our canonical and alternatively spliced CD28

Matched gene isoform IDs with Ensembl and RefSeq of our canonical and alternative spliced genes of CD28

UniProt-id	ENSG	ENST	ENSP
P10747-1	ENSG00000178562.18	ENST00000324106.9	ENSP00000324890.7
P10747-2	ENSG00000178562.18	ENST00000374481.7	ENSP00000363605.4
P10747-7	ENSG00000178562.18	ENST00000458610.6	ENSP00000393648.2

UniProt-id	NM ID	NP ID
P10747-1	NM_006139.3	NP_006130.1
P10747-2	NM_001243078.1	NP_001230007.1
P10747-4	NM_001243077.1	NP_001230006.1

Amino acid sequences of our canonical and alternatively spliced CD28

accession_id	Protein sequence
P10747-1	MLRLLLALNLFPSIQVTGNKILVKQSPMLVAYDNAVNLSCKYSYNLFSREFRASLHKGLDSAVEVCVVYGNYSQQLQVYSKTGFNCDGKL GNESVTFYLQNLYVNQTDIYFCKIEVMYPPPYLDNEKSNGTIIHVKGKHLCPSPLFPGPSKPFWVLVVVGGVLACYSLLVTVAFIIFWVR
P10747-2	MLRLLLALNLFPSIQVTGKHLCPSPLFPGPSKPFWVLVVVGGVLACYSLLVTVAFIIFWVRSKRSRLLHSDYMNMTPRRPGPTRKHYQPY
P10747-3	MLRLLLALNLFPSIQVTGNKILVKQSPMLVAYDNAVNLSYNEKSNGTIIHVKGKHLCPSPLFPGPSKPFWVLVVVGGVLACYSLLVTVAF
P10747-4	MLRLLLALNLFPSIQVTGNKILVKQSPMLVAYDNAVNLSWKHLCPSPLFPGPSKPFWVLVVVGGVLACYSLLVTVAFIIFWVRSKRSRLL
P10747-5
P10747-6
P10747-7	MPCGLSALIMCPKGMVAVVVAVDDGDSQALAGNKILVKQSPMLVAYDNAVNLSCKYSYNLFSREFRASLHKGLDSAVEVCVVYGNYSQQL QVYSKTGFNCDGKLGNESVTFYLQNLYVNQTDIYFCKIEVMYPPPYLDNEKSNGTIIHVKGKHLCPSPLFPGPSKPFWVLVVVGGVLACY

Protein Functional Features

Main function of this protein. (from UniProt)

CD28 (go to UniProt):P10747

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
P10747	Topological domain	19	152	Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255	Type=Deletion;Start=19;End=137
P10747	Topological domain	19	152	Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255	Type=Substitution;Start=40;End=124
P10747	Topological domain	19	152	Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255	Type=Substitution;Start=40;End=137
P10747	Topological domain	19	152	Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255	Type=Substitution;Start=40;End=124
P10747	Topological domain	19	152	Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255	Type=Substitution;Start=138;End=139
P10747	Topological domain	19	152	Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255	Type=Deletion;Start=140;End=220
P10747	Topological domain	19	152	Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255	Type=Substitution;Start=40;End=124
P10747	Topological domain	19	152	Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255	Type=Deletion;Start=152;End=207
P10747	Transmembrane	153	179	Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255	Type=Deletion;Start=140;End=220
P10747	Transmembrane	153	179	Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255	Type=Deletion;Start=152;End=207
P10747	Topological domain	180	220	Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255	Type=Deletion;Start=140;End=220
P10747	Topological domain	180	220	Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255	Type=Deletion;Start=152;End=207
P10747	Domain	28	137	Note=Ig-like V-type	Type=Deletion;Start=19;End=137
P10747	Domain	28	137	Note=Ig-like V-type	Type=Substitution;Start=40;End=124
P10747	Domain	28	137	Note=Ig-like V-type	Type=Substitution;Start=40;End=137
P10747	Domain	28	137	Note=Ig-like V-type	Type=Substitution;Start=40;End=124
P10747	Domain	28	137	Note=Ig-like V-type	Type=Substitution;Start=40;End=124
P10747	Region	198	220	Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Deletion;Start=140;End=220
P10747	Region	198	220	Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Deletion;Start=152;End=207

Gene Isoform Structures and Expression Levels for CD28

Gene structures of our canonical and alternative spliced genes of CD28
* 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 P10747-1

3D view using mol* of P10747-2

3D view using mol* of P10747-3

3D view using mol* of P10747-4

3D view using mol* of P10747-5

3D view using mol* of P10747-6

3D view using mol* of P10747-7

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 P10747-1

pLDDT distribution across the protein length of P10747-3

pLDDT distribution across the protein length of P10747-4

pLDDT distribution across the protein length of P10747-5

pLDDT distribution across the protein length of P10747-6

pLDDT distribution across the protein length of P10747-7

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 P10747-1

Ramachandran plot of P10747-2

Ramachandran plot of P10747-3

Ramachandran plot of P10747-4

Ramachandran plot of P10747-5

Ramachandran plot of P10747-6

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
P10747-1	0.695	38	0.617	72.373	0.578	0.662	0.987	0.985	1.103	0.893	1.179	20,56,60,61,111,112,113,124,125,126,127,128
P10747-3	0.789	60	0.727	127.939	0.586	0.63	0.921	0.294	1.163	0.253	0.641	29,30,31,32,33,34,35,36,51,52,53,54,55,56
P10747-4	0.894	67	0.917	144.06	0.55	0.657	0.967	0.741	0.757	0.979	1.174	27,28,29,30,36,37,38,39,40,41,42
P10747-5	0.877	88	0.919	158.123	0.678	0.53	0.759	0.494	0.86	0.575	0.628	20,21,22,23,24,25,26,27,28,29,44,45,46,47,48,49,50 ,51
P10747-6	0.498	22	0.445	40.131	0.794	0.481	0.672	0.369	0.872	0.423	0.583	9,10,11,12,13,24,25,26,27,28
P10747-7	0.673	36	0.665	119.364	0.746	0.549	0.727	0.608	0.701	0.868	1.617	29,30,31,32,33,34,35,36,57,58,137,140

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 P10747-1_P10747-1_6o8d_C.pdb

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

3D view using mol* of P10747-1_6o8d_C_P10747-2.pdb

3D view using mol* of P10747-1_6o8d_C_P10747-3.pdb

3D view using mol* of P10747-1_6o8d_C_P10747-4.pdb

3D view using mol* of P10747-1_6o8d_C_P10747-5.pdb

3D view using mol* of P10747-1_6o8d_C_P10747-6.pdb

3D view using mol* of P10747-1_6o8d_C_P10747-7.pdb

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

3D view using mol* of P10747-1_P10747-2.pdb

3D view using mol* of P10747-1_P10747-3.pdb

3D view using mol* of P10747-1_P10747-4.pdb

3D view using mol* of P10747-1_P10747-5.pdb

3D view using mol* of P10747-1_P10747-6.pdb

3D view using mol* of P10747-1_P10747-7.pdb

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

./stats/secondary_structure/figure/P10747-1_vs_P10747-2.png