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:MYD88

Protein Summary

Gene summary

Gene name: MYD88
ASpdb.0 ID: 4615
	Gene
Gene symbol	MYD88
Gene ID	4615
Gene name	MYD88 innate immune signal transduction adaptor
Synonyms	IMD68\|MYD88D\|WM1
Cytomap	3p22.2
Type of gene	protein-coding
Description	myeloid differentiation primary response protein MyD88TLR adaptor MYD88mutant myeloid differentiation primary response 88myeloid differentiation primary response 88myeloid differentiation primary response gene (88)
Modification date	20240411
UniProtAcc	Q99836

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

Partner	Gene	GO ID	GO term	PubMed ID
Gene	MYD88	GO:0005634	nucleus	22155231
Gene	MYD88	GO:0005737	cytoplasm	9430229
Gene	MYD88	GO:0005737	cytoplasm	22155231
Gene	MYD88	GO:0005886	plasma membrane	16751103
Gene	MYD88	GO:0009986	cell surface	22851693
Gene	MYD88	GO:0019897	extrinsic component of plasma membrane	9430229
Gene	MYD88	GO:0031234	extrinsic component of cytoplasmic side of plasma membrane	16751103
Gene	MYD88	GO:0032731	positive regulation of interleukin-1 beta production	33718825
Gene	MYD88	GO:0034142	toll-like receptor 4 signaling pathway	16751103
Gene	MYD88	GO:0034158	toll-like receptor 8 signaling pathway	33718825
Gene	MYD88	GO:0035591	signaling adaptor activity	16751103
Gene	MYD88	GO:0038172	interleukin-33-mediated signaling pathway	18802081
Gene	MYD88	GO:0051607	defense response to virus	33718825
Gene	MYD88	GO:0060090	molecular adaptor activity	9430229\|9734363\|16751103
Gene	MYD88	GO:0070498	interleukin-1-mediated signaling pathway	9430229
Gene	MYD88	GO:0070935	3'-UTR-mediated mRNA stabilization	15294994

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
Q99836-1	Q99836-1_4eo7_A.pdb	4EO7	X-ray	1.45	A	157	296

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
Q99836	MYD88	Q99836-1	Q99836-2	296	251	110	154	Deletion	none	none	109	109
Q99836	MYD88	Q99836-1	Q99836-3	296	191	156	296	Substitution	HMPERFDAFICYCPSDIQFVQEMIRQLEQTNYRLKLCVSDRDVLPGTCVWSIASELIEKRCRRMVVVVSDDYLQSKECDFQTKFALSLSPGAHQKRLIPIKYKAMKKEFPSILRFITVCDYTNPCTKSWFWTRLAKALSLP	AAGWWWLSLMITCRARNVTSRPNLHSASLQVPIRSD	156	191
Q99836	MYD88	Q99836-1	Q99836-4	296	146	110	110	Substitution	E	G	110	110
Q99836	MYD88	Q99836-1	Q99836-4	296	146	111	155	Deletion	none	none	110	110
Q99836	MYD88	Q99836-1	Q99836-4	296	146	156	296	Substitution	HMPERFDAFICYCPSDIQFVQEMIRQLEQTNYRLKLCVSDRDVLPGTCVWSIASELIEKRCRRMVVVVSDDYLQSKECDFQTKFALSLSPGAHQKRLIPIKYKAMKKEFPSILRFITVCDYTNPCTKSWFWTRLAKALSLP	AAGWWWLSLMITCRARNVTSRPNLHSASLQVPIRSD	111	146
Q99836	MYD88	Q99836-1	Q99836-5	296	275	1	22	Substitution	MAAGGPGAGSAAPVSSTSSLPL	M	1	1
Q99836	MYD88	Q99836-1	Q99836-6	296	304	215	215	Substitution	R	RLARRPRGG	215	223

Multiple sequence alignment of our canonical and alternatively spliced MYD88

Matched gene isoform IDs with Ensembl and RefSeq of our canonical and alternative spliced genes of MYD88

UniProt-id	ENSG	ENST	ENSP
Q99836-1	ENSG00000172936.18	ENST00000650905.2	ENSP00000498360.2
Q99836-2	ENSG00000172936.18	ENST00000417037.8	ENSP00000401399.4
Q99836-3	ENSG00000172936.18	ENST00000651800.2	ENSP00000499012.2
Q99836-4	ENSG00000172936.18	ENST00000650112.2	ENSP00000497991.2
Q99836-6	ENSG00000172936.18	ENST00000421516.3	ENSP00000391753.3

UniProt-id	NM ID	NP ID
Q99836-1	NM_002468.4	NP_002459.2
Q99836-2	NM_001172568.1	NP_001166039.1
Q99836-3	NM_001172569.1	NP_001166040.1
Q99836-4	NM_001172566.1	NP_001166037.1

Amino acid sequences of our canonical and alternatively spliced MYD88

accession_id	Protein sequence
Q99836-1	MAAGGPGAGSAAPVSSTSSLPLAALNMRVRRRLSLFLNVRTQVAADWTALAEEMDFEYLEIRQLETQADPTGRLLDAWQGRPGASVGRLL ELLTKLGRDDVLLELGPSIEEDCQKYILKQQQEEAEKPLQVAAVDSSVPRTAELAGITTLDDPLGHMPERFDAFICYCPSDIQFVQEMIR QLEQTNYRLKLCVSDRDVLPGTCVWSIASELIEKRCRRMVVVVSDDYLQSKECDFQTKFALSLSPGAHQKRLIPIKYKAMKKEFPSILRF
Q99836-2	MAAGGPGAGSAAPVSSTSSLPLAALNMRVRRRLSLFLNVRTQVAADWTALAEEMDFEYLEIRQLETQADPTGRLLDAWQGRPGASVGRLL ELLTKLGRDDVLLELGPSIGHMPERFDAFICYCPSDIQFVQEMIRQLEQTNYRLKLCVSDRDVLPGTCVWSIASELIEKRCRRMVVVVSD
Q99836-3	MAAGGPGAGSAAPVSSTSSLPLAALNMRVRRRLSLFLNVRTQVAADWTALAEEMDFEYLEIRQLETQADPTGRLLDAWQGRPGASVGRLL ELLTKLGRDDVLLELGPSIEEDCQKYILKQQQEEAEKPLQVAAVDSSVPRTAELAGITTLDDPLGAAGWWWLSLMITCRARNVTSRPNLH
Q99836-4	MAAGGPGAGSAAPVSSTSSLPLAALNMRVRRRLSLFLNVRTQVAADWTALAEEMDFEYLEIRQLETQADPTGRLLDAWQGRPGASVGRLL
Q99836-5	MAALNMRVRRRLSLFLNVRTQVAADWTALAEEMDFEYLEIRQLETQADPTGRLLDAWQGRPGASVGRLLELLTKLGRDDVLLELGPSIEE DCQKYILKQQQEEAEKPLQVAAVDSSVPRTAELAGITTLDDPLGHMPERFDAFICYCPSDIQFVQEMIRQLEQTNYRLKLCVSDRDVLPG TCVWSIASELIEKRCRRMVVVVSDDYLQSKECDFQTKFALSLSPGAHQKRLIPIKYKAMKKEFPSILRFITVCDYTNPCTKSWFWTRLAK
Q99836-6	MAAGGPGAGSAAPVSSTSSLPLAALNMRVRRRLSLFLNVRTQVAADWTALAEEMDFEYLEIRQLETQADPTGRLLDAWQGRPGASVGRLL ELLTKLGRDDVLLELGPSIEEDCQKYILKQQQEEAEKPLQVAAVDSSVPRTAELAGITTLDDPLGHMPERFDAFICYCPSDIQFVQEMIR QLEQTNYRLKLCVSDRDVLPGTCVWSIASELIEKRLARRPRGGCRRMVVVVSDDYLQSKECDFQTKFALSLSPGAHQKRLIPIKYKAMKK

Protein Functional Features

Main function of this protein. (from UniProt)

MYD88 (go to UniProt):Q99836

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
Q99836	Domain	159	293	Note=TIR;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00204	Type=Substitution;Start=156;End=296
Q99836	Domain	159	293	Note=TIR;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00204	Type=Substitution;Start=156;End=296
Q99836	Domain	159	293	Note=TIR;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00204	Type=Substitution;Start=215;End=215
Q99836	Region	110	155	Note=Intermediate domain;Ontology_term=ECO:0000250;evidence=ECO:0000250	Type=Deletion;Start=110;End=154
Q99836	Region	110	155	Note=Intermediate domain;Ontology_term=ECO:0000250;evidence=ECO:0000250	Type=Substitution;Start=110;End=110
Q99836	Region	110	155	Note=Intermediate domain;Ontology_term=ECO:0000250;evidence=ECO:0000250	Type=Deletion;Start=111;End=155

Gene Isoform Structures and Expression Levels for MYD88

Gene structures of our canonical and alternative spliced genes of MYD88
* 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 Q99836-1

3D view using mol* of Q99836-2

3D view using mol* of Q99836-3

3D view using mol* of Q99836-4

3D view using mol* of Q99836-5

3D view using mol* of Q99836-6

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 Q99836-1

pLDDT distribution across the protein length of Q99836-2

pLDDT distribution across the protein length of Q99836-3

pLDDT distribution across the protein length of Q99836-4

pLDDT distribution across the protein length of Q99836-5

pLDDT distribution across the protein length of Q99836-6

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 Q99836-1

Ramachandran plot of Q99836-3

Ramachandran plot of Q99836-4

Ramachandran plot of Q99836-5

Ramachandran plot of Q99836-6

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
Q99836-1	0.968	172	1.003	406.798	0.619	0.626	0.854	0.544	0.957	0.569	0.885	160,161,162,213,214,215,216,217,218,241,244,246,24 7,248,249,250,251,252,253,254,270,271,272,273,274, 275,278,281,284,285,288,289,291,292,294,295,296
Q99836-2	0.98	147	0.978	409.542	0.664	0.668	0.885	0.297	1.111	0.267	0.766	23,24,25,26,27,28,29,30,31,32,34,69,72,75,76,79,10 4,105,107,108,112,119,120,121,122,124,127,148,149, 150,151,152,153,154,155,156,157,160,161,162,163,16 4,165,187,190
Q99836-3	0.876	54	0.905	162.239	0.561	0.668	0.926	1.505	0.573	2.625	5.014	13,14,17,18,87,90,91,93,101,102,105,106,107,109,11 0
Q99836-4	1.078	90	1.144	220.549	0.451	0.742	1.025	1.884	0.593	3.179	1.536	13,14,15,17,18,87,90,91,94,109,110,111,112,113,116 ,117,120
Q99836-5	0.76	50	0.738	205.457	0.764	0.629	0.846	0.399	0.933	0.427	0.967	197,228,229,231,232,250,251,253,254,260,264,267,27 1,275
Q99836-6	0.883	68	0.878	180.075	0.518	0.69	0.987	0.647	0.954	0.678	0.851	224,226,249,252,253,254,255,257,258,259,260,261,27 8,279,280,282,296,300,303,304

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 Q99836-1_Q99836-1_4eo7_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 Q99836-1_4eo7_A_Q99836-2.pdb

3D view using mol* of Q99836-1_4eo7_A_Q99836-3.pdb

3D view using mol* of Q99836-1_4eo7_A_Q99836-4.pdb

3D view using mol* of Q99836-1_4eo7_A_Q99836-5.pdb

3D view using mol* of Q99836-1_4eo7_A_Q99836-6.pdb

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

3D view using mol* of Q99836-1_Q99836-2.pdb

3D view using mol* of Q99836-1_Q99836-3.pdb

3D view using mol* of Q99836-1_Q99836-4.pdb

3D view using mol* of Q99836-1_Q99836-5.pdb

3D view using mol* of Q99836-1_Q99836-6.pdb

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

./stats/secondary_structure/figure/Q99836-1_vs_Q99836-2.png