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:IYD

Protein Summary

Gene summary

Gene name: IYD
ASpdb.0 ID: 389434
	Gene
Gene symbol	IYD
Gene ID	389434
Gene name	iodotyrosine deiodinase
Synonyms	C6orf71\|DEHAL1\|IYD-1\|TDH4
Cytomap	6q25.1
Type of gene	protein-coding
Description	iodotyrosine deiodinase 1iodotyrosine dehalogenase 1
Modification date	20240411
UniProtAcc	Q6PHW0

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

Partner	Gene	GO ID	GO term	PubMed ID
Gene	IYD	GO:0005654	nucleoplasm	-
Gene	IYD	GO:0005886	plasma membrane	15289438
Gene	IYD	GO:0006570	tyrosine metabolic process	25395621\|28157283
Gene	IYD	GO:0010181	FMN binding	25395621\|28157283
Gene	IYD	GO:0030659	cytoplasmic vesicle membrane	15289438
Gene	IYD	GO:0042403	thyroid hormone metabolic process	25395621
Gene	IYD	GO:0140616	iodotyrosine deiodinase activity	15289438\|25395621\|28157283

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
Q6PHW0-1	Q6PHW0-1_5yak_B.pdb	5YAK	X-ray	2.3	B	71	289

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
Q6PHW0	IYD	Q6PHW0-1	Q6PHW0-3	289	247	230	248	Substitution	NAGLVTVTTTPLNCGPRLR	VFGKIILKELALISFLNL	230	247
Q6PHW0	IYD	Q6PHW0-1	Q6PHW0-3	289	247	249	289	Deletion	none	none	247	247
Q6PHW0	IYD	Q6PHW0-1	Q6PHW0-4	289	293	230	289	Substitution	NAGLVTVTTTPLNCGPRLRVLLGRPAHEKLLMLLPVGYPSKEATVPDLKRKPLDQIMVTV	VNNGITMRHQTARHRHLIEGPGRSSEACSKLSSQGCPECRSGDCHYHSSQLWPSTEGAPGPPRT	230	293
Q6PHW0	IYD	Q6PHW0-1	Q6PHW0-5	289	284	230	284	Substitution	NAGLVTVTTTPLNCGPRLRVLLGRPAHEKLLMLLPVGYPSKEATVPDLKRKPLDQ	VNNGITMRHQTARHRHLIEGPGRSSEACSKLSSQGRPGASAAGSLFHFAIEFAAP	230	284
Q6PHW0	IYD	Q6PHW0-1	Q6PHW0-5	289	284	285	289	Deletion	none	none	284	284
Q6PHW0	IYD	Q6PHW0-1	Q6PHW0-6	289	270	230	270	Substitution	NAGLVTVTTTPLNCGPRLRVLLGRPAHEKLLMLLPVGYPSK	VNNGITMRHQTARHRHLIEGPGRSSEACSKLSSQGRPGFYC	230	270
Q6PHW0	IYD	Q6PHW0-1	Q6PHW0-6	289	270	271	289	Deletion	none	none	270	270
Q6PHW0	IYD	Q6PHW0-1	Q6PHW0-7	289	192	1	55	Deletion	none	none	0	0
Q6PHW0	IYD	Q6PHW0-1	Q6PHW0-7	289	192	56	61	Substitution	QAEEDA	MKEADV	1	6
Q6PHW0	IYD	Q6PHW0-1	Q6PHW0-7	289	192	230	248	Substitution	NAGLVTVTTTPLNCGPRLR	VFGKIILKELALISFLNL	175	192
Q6PHW0	IYD	Q6PHW0-1	Q6PHW0-7	289	192	249	289	Deletion	none	none	192	192

Multiple sequence alignment of our canonical and alternatively spliced IYD

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

UniProt-id	ENSG	ENST	ENSP
Q6PHW0-1	ENSG00000009765.15	ENST00000344419.8	ENSP00000343763.4
Q6PHW0-3	ENSG00000009765.15	ENST00000367335.7	ENSP00000356304.3
Q6PHW0-3	ENSG00000009765.15	ENST00000392256.6	ENSP00000376085.2
Q6PHW0-4	ENSG00000009765.15	ENST00000229447.9	ENSP00000229447.5

UniProt-id	NM ID	NP ID
Q6PHW0-1	NM_203395.2	NP_981932.1
Q6PHW0-3	NM_001164695.1	NP_001158167.1
Q6PHW0-4	NM_001164694.1	NP_001158166.1

Amino acid sequences of our canonical and alternatively spliced IYD

accession_id	Protein sequence
Q6PHW0-1	MYFLTPILVAILCILVVWIFKNADRSMEKKKGEPRTRAEARPWVDEDLKDSSDLHQAEEDADEWQESEENVEHIPFSHNHYPEKEMVKRS QEFYELLNKRRSVRFISNEQVPMEVIDNVIRTAGTAPSGAHTEPWTFVVVKDPDVKHKIRKIIEEEEEINYMKRMGHRWVTDLKKLRTNW IKEYLDTAPILILIFKQVHGFAANGKKKVHYYNEISVSIACGILLAALQNAGLVTVTTTPLNCGPRLRVLLGRPAHEKLLMLLPVGYPSK
Q6PHW0-3	MYFLTPILVAILCILVVWIFKNADRSMEKKKGEPRTRAEARPWVDEDLKDSSDLHQAEEDADEWQESEENVEHIPFSHNHYPEKEMVKRS QEFYELLNKRRSVRFISNEQVPMEVIDNVIRTAGTAPSGAHTEPWTFVVVKDPDVKHKIRKIIEEEEEINYMKRMGHRWVTDLKKLRTNW
Q6PHW0-4	MYFLTPILVAILCILVVWIFKNADRSMEKKKGEPRTRAEARPWVDEDLKDSSDLHQAEEDADEWQESEENVEHIPFSHNHYPEKEMVKRS QEFYELLNKRRSVRFISNEQVPMEVIDNVIRTAGTAPSGAHTEPWTFVVVKDPDVKHKIRKIIEEEEEINYMKRMGHRWVTDLKKLRTNW IKEYLDTAPILILIFKQVHGFAANGKKKVHYYNEISVSIACGILLAALQVNNGITMRHQTARHRHLIEGPGRSSEACSKLSSQGCPECRS
Q6PHW0-5	MYFLTPILVAILCILVVWIFKNADRSMEKKKGEPRTRAEARPWVDEDLKDSSDLHQAEEDADEWQESEENVEHIPFSHNHYPEKEMVKRS QEFYELLNKRRSVRFISNEQVPMEVIDNVIRTAGTAPSGAHTEPWTFVVVKDPDVKHKIRKIIEEEEEINYMKRMGHRWVTDLKKLRTNW IKEYLDTAPILILIFKQVHGFAANGKKKVHYYNEISVSIACGILLAALQVNNGITMRHQTARHRHLIEGPGRSSEACSKLSSQGRPGASA
Q6PHW0-6	MYFLTPILVAILCILVVWIFKNADRSMEKKKGEPRTRAEARPWVDEDLKDSSDLHQAEEDADEWQESEENVEHIPFSHNHYPEKEMVKRS QEFYELLNKRRSVRFISNEQVPMEVIDNVIRTAGTAPSGAHTEPWTFVVVKDPDVKHKIRKIIEEEEEINYMKRMGHRWVTDLKKLRTNW IKEYLDTAPILILIFKQVHGFAANGKKKVHYYNEISVSIACGILLAALQVNNGITMRHQTARHRHLIEGPGRSSEACSKLSSQGRPGFYC
Q6PHW0-7	MKEADVDEWQESEENVEHIPFSHNHYPEKEMVKRSQEFYELLNKRRSVRFISNEQVPMEVIDNVIRTAGTAPSGAHTEPWTFVVVKDPDV KHKIRKIIEEEEEINYMKRMGHRWVTDLKKLRTNWIKEYLDTAPILILIFKQVHGFAANGKKKVHYYNEISVSIACGILLAALQVFGKII

Protein Functional Features

Main function of this protein. (from UniProt)

IYD (go to UniProt):Q6PHW0

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
Q6PHW0	Transmembrane	1	21	Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255	Type=Deletion;Start=1;End=55
Q6PHW0	Region	29	69	Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Deletion;Start=1;End=55
Q6PHW0	Region	29	69	Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Substitution;Start=56;End=61
Q6PHW0	Compositional bias	29	58	Note=Basic and acidic residues;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Deletion;Start=1;End=55
Q6PHW0	Compositional bias	29	58	Note=Basic and acidic residues;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Substitution;Start=56;End=61

Gene Isoform Structures and Expression Levels for IYD

Gene structures of our canonical and alternative spliced genes of IYD
* 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 Q6PHW0-1

3D view using mol* of Q6PHW0-3

3D view using mol* of Q6PHW0-4

3D view using mol* of Q6PHW0-5

3D view using mol* of Q6PHW0-6

3D view using mol* of Q6PHW0-7

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 Q6PHW0-1

pLDDT distribution across the protein length of Q6PHW0-3

pLDDT distribution across the protein length of Q6PHW0-4

pLDDT distribution across the protein length of Q6PHW0-5

pLDDT distribution across the protein length of Q6PHW0-6

pLDDT distribution across the protein length of Q6PHW0-7

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 Q6PHW0-1

Ramachandran plot of Q6PHW0-4

Ramachandran plot of Q6PHW0-5

Ramachandran plot of Q6PHW0-6

Ramachandran plot of Q6PHW0-7

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
Q6PHW0-1	0.988	183	0.974	378.672	0.517	0.681	0.916	0.265	1.148	0.231	0.512	45,102,103,104,105,106,153,157,160,161,165,169,173 ,175,176,177,178,179,181,182,183,184,187,236,237,2 38,239,240,241,269,273,274,275
Q6PHW0-3	1.02	193	1.07	605.738	0.63	0.665	0.798	0.716	0.826	0.867	0.684	100,101,102,103,104,105,106,149,152,153,156,157,16 0,176,177,178,179,181,182,183,184,185,187,193,194, 221,224,225,228,236,239,240,241,242,243,244,245,24 6,247
Q6PHW0-4	1.028	105	0.999	207.172	0.49	0.74	1.01	0.338	1.181	0.286	1.005	56,57,60,61,63,64,65,68,130,132,206,207,208,209,21 1
Q6PHW0-5	1.037	70	0.979	142.345	0.478	0.933	1.375	1.413	1.126	1.255	1.004	106,116,149,153,184,185,188,190,191,192,193,194,21 7,221,224,274,275,276,277,278,279,281
Q6PHW0-6	1.047	687	1.074	2068.29	0.482	0.745	0.967	0.827	0.962	0.86	0.887	12,13,15,16,17,19,20,21,23,24,27,96,97,98,99,100,1 01,102,103,104,105,106,107,109,111,116,138,140,145 ,148,149,152,153,155,156,157,160,161,164,165,169,1 72,173,175,176,177,178,179,181,182,183,184,185,187 ,188,189,190,191,192,193,194,195,196,218,224,225,2 28,229,232,233,234,235,236,239,243,246,247,249,251 ,252,253,254,255,256,257,258,259,260,261,263,264,2 65,266,267,268,269,270
Q6PHW0-7	1.025	104	1.01	192.08	0.453	0.736	1.022	0.727	1.139	0.638	0.994	7,8,9,10,13,14,75,77,147,149,151,152,153,154,156

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 Q6PHW0-1_Q6PHW0-1_5yak_B.pdb

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

3D view using mol* of Q6PHW0-1_5yak_B_Q6PHW0-3.pdb

3D view using mol* of Q6PHW0-1_5yak_B_Q6PHW0-4.pdb

3D view using mol* of Q6PHW0-1_5yak_B_Q6PHW0-5.pdb

3D view using mol* of Q6PHW0-1_5yak_B_Q6PHW0-6.pdb

3D view using mol* of Q6PHW0-1_5yak_B_Q6PHW0-7.pdb

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

3D view using mol* of Q6PHW0-1_Q6PHW0-3.pdb

3D view using mol* of Q6PHW0-1_Q6PHW0-4.pdb

3D view using mol* of Q6PHW0-1_Q6PHW0-5.pdb

3D view using mol* of Q6PHW0-1_Q6PHW0-6.pdb

3D view using mol* of Q6PHW0-1_Q6PHW0-7.pdb

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

./stats/secondary_structure/figure/Q6PHW0-1_vs_Q6PHW0-3.png