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:SLC3A1

Protein Summary

Gene summary

Gene name: SLC3A1
ASpdb.0 ID: 6519
	Gene
Gene symbol	SLC3A1
Gene ID	6519
Gene name	solute carrier family 3 member 1
Synonyms	ATR1\|CSNU1\|D2H\|NBAT\|RBAT
Cytomap	2p21
Type of gene	protein-coding
Description	amino acid transporter heavy chain SLC3A1B(0,+)-type amino acid transport proteinamino acid transporter 1b(0,+)-type amino acid transporter-related heavy chainneutral and basic amino acid transport protein rBATsolute carrier family 3 (amino acid tran
Modification date	20240411
UniProtAcc	Q07837

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

Partner	Gene	GO ID	GO term	PubMed ID
Gene	SLC3A1	GO:0031526	brush border membrane	12167606
Gene	SLC3A1	GO:0046982	protein heterodimerization activity	32494597

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
Q07837-1	Q07837-1_6li9_A.pdb	6LI9	EM	2.3	A	63	685

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
Q07837	SLC3A1	Q07837-1	Q07837-2	685	407	1	278	Deletion	none	none	0	0
Q07837	SLC3A1	Q07837-1	Q07837-3	685	391	380	391	Substitution	FMGTEAYAESID	LTTAYALISSQA	380	391
Q07837	SLC3A1	Q07837-1	Q07837-3	685	391	392	685	Deletion	none	none	391	391
Q07837	SLC3A1	Q07837-1	Q07837-4	685	316	1	8	Substitution	MAEDKSKR	MTLNLVNS	1	8
Q07837	SLC3A1	Q07837-1	Q07837-4	685	316	9	377	Deletion	none	none	8	8
Q07837	SLC3A1	Q07837-1	Q07837-5	685	502	501	502	Substitution	NT	VS	501	502
Q07837	SLC3A1	Q07837-1	Q07837-5	685	502	503	685	Deletion	none	none	502	502
Q07837	SLC3A1	Q07837-1	Q07837-6	685	564	541	564	Substitution	QKTQPRSALKLYQDLSLLHANELL	SISENFMLILETKKWVSTESTHSP	541	564
Q07837	SLC3A1	Q07837-1	Q07837-6	685	564	565	685	Deletion	none	none	564	564
Q07837	SLC3A1	Q07837-1	Q07837-7	685	551	541	551	Substitution	QKTQPRSALKL	LLRHPCSSAVA	541	551
Q07837	SLC3A1	Q07837-1	Q07837-7	685	551	552	685	Deletion	none	none	551	551

Multiple sequence alignment of our canonical and alternatively spliced SLC3A1

Matched gene isoform IDs with Ensembl and RefSeq of our canonical and alternative spliced genes of SLC3A1

UniProt-id	ENSG	ENST	ENSP
Q07837-1	ENSG00000138079.14	ENST00000260649.11	ENSP00000260649.6
Q07837-2	ENSG00000138079.14	ENST00000409380.5	ENSP00000386709.1
Q07837-3	ENSG00000138079.14	ENST00000410056.7	ENSP00000387337.3
Q07837-4	ENSG00000138079.14	ENST00000409740.3	ENSP00000386677.3
Q07837-5	ENSG00000138079.14	ENST00000409741.5	ENSP00000386954.1
Q07837-6	ENSG00000138079.14	ENST00000409229.7	ENSP00000386620.3

UniProt-id	NM ID	NP ID
Q07837-1	NM_000341.3	NP_000332.2

Amino acid sequences of our canonical and alternatively spliced SLC3A1

accession_id	Protein sequence
Q07837-1	MAEDKSKRDSIEMSMKGCQTNNGFVHNEDILEQTPDPGSSTDNLKHSTRGILGSQEPDFKGVQPYAGMPKEVLFQFSGQARYRIPREILF WLTVASVLVLIAATIAIIALSPKCLDWWQEGPMYQIYPRSFKDSNKDGNGDLKGIQDKLDYITALNIKTVWITSFYKSSLKDFRYGVEDF REVDPIFGTMEDFENLVAAIHDKGLKLIIDFIPNHTSDKHIWFQLSRTRTGKYTDYYIWHDCTHENGKTIPPNNWLSVYGNSSWHFDEVR NQCYFHQFMKEQPDLNFRNPDVQEEIKEILRFWLTKGVDGFSLDAVKFLLEAKHLRDEIQVNKTQIPDTVTQYSELYHDFTTTQVGMHDI VRSFRQTMDQYSTEPGRYRFMGTEAYAESIDRTVMYYGLPFIQEADFPFNNYLSMLDTVSGNSVYEVITSWMENMPEGKWPNWMIGGPDS SRLTSRLGNQYVNVMNMLLFTLPGTPITYYGEEIGMGNIVAANLNESYDINTLRSKSPMQWDNSSNAGFSEASNTWLPTNSDYHTVNVDV QKTQPRSALKLYQDLSLLHANELLLNRGWFCHLRNDSHYVVYTRELDGIDRIFIVVLNFGESTLLNLHNMISGLPAKMRIRLSTNSADKG
Q07837-2	MKEQPDLNFRNPDVQEEIKEILRFWLTKGVDGFSLDAVKFLLEAKHLRDEIQVNKTQIPDTVTQYSELYHDFTTTQVGMHDIVRSFRQTM DQYSTEPGRYRFMGTEAYAESIDRTVMYYGLPFIQEADFPFNNYLSMLDTVSGNSVYEVITSWMENMPEGKWPNWMIGGPDSSRLTSRLG NQYVNVMNMLLFTLPGTPITYYGEEIGMGNIVAANLNESYDINTLRSKSPMQWDNSSNAGFSEASNTWLPTNSDYHTVNVDVQKTQPRSA LKLYQDLSLLHANELLLNRGWFCHLRNDSHYVVYTRELDGIDRIFIVVLNFGESTLLNLHNMISGLPAKMRIRLSTNSADKGSKVDTSGI
Q07837-3	MAEDKSKRDSIEMSMKGCQTNNGFVHNEDILEQTPDPGSSTDNLKHSTRGILGSQEPDFKGVQPYAGMPKEVLFQFSGQARYRIPREILF WLTVASVLVLIAATIAIIALSPKCLDWWQEGPMYQIYPRSFKDSNKDGNGDLKGIQDKLDYITALNIKTVWITSFYKSSLKDFRYGVEDF REVDPIFGTMEDFENLVAAIHDKGLKLIIDFIPNHTSDKHIWFQLSRTRTGKYTDYYIWHDCTHENGKTIPPNNWLSVYGNSSWHFDEVR NQCYFHQFMKEQPDLNFRNPDVQEEIKEILRFWLTKGVDGFSLDAVKFLLEAKHLRDEIQVNKTQIPDTVTQYSELYHDFTTTQVGMHDI
Q07837-4	MTLNLVNSYRFMGTEAYAESIDRTVMYYGLPFIQEADFPFNNYLSMLDTVSGNSVYEVITSWMENMPEGKWPNWMIGGPDSSRLTSRLGN QYVNVMNMLLFTLPGTPITYYGEEIGMGNIVAANLNESYDINTLRSKSPMQWDNSSNAGFSEASNTWLPTNSDYHTVNVDVQKTQPRSAL KLYQDLSLLHANELLLNRGWFCHLRNDSHYVVYTRELDGIDRIFIVVLNFGESTLLNLHNMISGLPAKMRIRLSTNSADKGSKVDTSGIF
Q07837-5	MAEDKSKRDSIEMSMKGCQTNNGFVHNEDILEQTPDPGSSTDNLKHSTRGILGSQEPDFKGVQPYAGMPKEVLFQFSGQARYRIPREILF WLTVASVLVLIAATIAIIALSPKCLDWWQEGPMYQIYPRSFKDSNKDGNGDLKGIQDKLDYITALNIKTVWITSFYKSSLKDFRYGVEDF REVDPIFGTMEDFENLVAAIHDKGLKLIIDFIPNHTSDKHIWFQLSRTRTGKYTDYYIWHDCTHENGKTIPPNNWLSVYGNSSWHFDEVR NQCYFHQFMKEQPDLNFRNPDVQEEIKEILRFWLTKGVDGFSLDAVKFLLEAKHLRDEIQVNKTQIPDTVTQYSELYHDFTTTQVGMHDI VRSFRQTMDQYSTEPGRYRFMGTEAYAESIDRTVMYYGLPFIQEADFPFNNYLSMLDTVSGNSVYEVITSWMENMPEGKWPNWMIGGPDS
Q07837-6	MAEDKSKRDSIEMSMKGCQTNNGFVHNEDILEQTPDPGSSTDNLKHSTRGILGSQEPDFKGVQPYAGMPKEVLFQFSGQARYRIPREILF WLTVASVLVLIAATIAIIALSPKCLDWWQEGPMYQIYPRSFKDSNKDGNGDLKGIQDKLDYITALNIKTVWITSFYKSSLKDFRYGVEDF REVDPIFGTMEDFENLVAAIHDKGLKLIIDFIPNHTSDKHIWFQLSRTRTGKYTDYYIWHDCTHENGKTIPPNNWLSVYGNSSWHFDEVR NQCYFHQFMKEQPDLNFRNPDVQEEIKEILRFWLTKGVDGFSLDAVKFLLEAKHLRDEIQVNKTQIPDTVTQYSELYHDFTTTQVGMHDI VRSFRQTMDQYSTEPGRYRFMGTEAYAESIDRTVMYYGLPFIQEADFPFNNYLSMLDTVSGNSVYEVITSWMENMPEGKWPNWMIGGPDS SRLTSRLGNQYVNVMNMLLFTLPGTPITYYGEEIGMGNIVAANLNESYDINTLRSKSPMQWDNSSNAGFSEASNTWLPTNSDYHTVNVDV
Q07837-7	MAEDKSKRDSIEMSMKGCQTNNGFVHNEDILEQTPDPGSSTDNLKHSTRGILGSQEPDFKGVQPYAGMPKEVLFQFSGQARYRIPREILF WLTVASVLVLIAATIAIIALSPKCLDWWQEGPMYQIYPRSFKDSNKDGNGDLKGIQDKLDYITALNIKTVWITSFYKSSLKDFRYGVEDF REVDPIFGTMEDFENLVAAIHDKGLKLIIDFIPNHTSDKHIWFQLSRTRTGKYTDYYIWHDCTHENGKTIPPNNWLSVYGNSSWHFDEVR NQCYFHQFMKEQPDLNFRNPDVQEEIKEILRFWLTKGVDGFSLDAVKFLLEAKHLRDEIQVNKTQIPDTVTQYSELYHDFTTTQVGMHDI VRSFRQTMDQYSTEPGRYRFMGTEAYAESIDRTVMYYGLPFIQEADFPFNNYLSMLDTVSGNSVYEVITSWMENMPEGKWPNWMIGGPDS SRLTSRLGNQYVNVMNMLLFTLPGTPITYYGEEIGMGNIVAANLNESYDINTLRSKSPMQWDNSSNAGFSEASNTWLPTNSDYHTVNVDV

Protein Functional Features

Main function of this protein. (from UniProt)

SLC3A1 (go to UniProt):Q07837

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
Q07837	Topological domain	1	87	Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255	Type=Deletion;Start=1;End=278
Q07837	Topological domain	1	87	Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255	Type=Substitution;Start=1;End=8
Q07837	Topological domain	1	87	Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255	Type=Deletion;Start=9;End=377
Q07837	Transmembrane	88	108	Note=Helical%3B Signal-anchor for type II membrane protein;Ontology_term=ECO:0000255;evidence=ECO:0000255	Type=Deletion;Start=1;End=278
Q07837	Transmembrane	88	108	Note=Helical%3B Signal-anchor for type II membrane protein;Ontology_term=ECO:0000255;evidence=ECO:0000255	Type=Deletion;Start=9;End=377
Q07837	Topological domain	109	685	Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255	Type=Deletion;Start=1;End=278
Q07837	Topological domain	109	685	Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255	Type=Substitution;Start=380;End=391
Q07837	Topological domain	109	685	Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255	Type=Deletion;Start=392;End=685
Q07837	Topological domain	109	685	Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255	Type=Deletion;Start=9;End=377
Q07837	Topological domain	109	685	Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255	Type=Substitution;Start=501;End=502
Q07837	Topological domain	109	685	Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255	Type=Deletion;Start=503;End=685
Q07837	Topological domain	109	685	Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255	Type=Substitution;Start=541;End=564
Q07837	Topological domain	109	685	Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255	Type=Deletion;Start=565;End=685
Q07837	Topological domain	109	685	Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255	Type=Substitution;Start=541;End=551
Q07837	Topological domain	109	685	Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255	Type=Deletion;Start=552;End=685
Q07837	Region	1	56	Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Deletion;Start=1;End=278
Q07837	Region	1	56	Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Substitution;Start=1;End=8
Q07837	Region	1	56	Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Deletion;Start=9;End=377
Q07837	Compositional bias	13	50	Note=Polar residues;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Deletion;Start=1;End=278
Q07837	Compositional bias	13	50	Note=Polar residues;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Deletion;Start=9;End=377

Gene Isoform Structures and Expression Levels for SLC3A1

Gene structures of our canonical and alternative spliced genes of SLC3A1
* 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 Q07837-1

3D view using mol* of Q07837-2

3D view using mol* of Q07837-3

3D view using mol* of Q07837-4

3D view using mol* of Q07837-5

3D view using mol* of Q07837-6

3D view using mol* of Q07837-7

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 Q07837-1

pLDDT distribution across the protein length of Q07837-2

pLDDT distribution across the protein length of Q07837-3

pLDDT distribution across the protein length of Q07837-4

pLDDT distribution across the protein length of Q07837-5

pLDDT distribution across the protein length of Q07837-6

pLDDT distribution across the protein length of Q07837-7

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 Q07837-1

Ramachandran plot of Q07837-2

Ramachandran plot of Q07837-3

Ramachandran plot of Q07837-5

Ramachandran plot of Q07837-6

Ramachandran plot of Q07837-7

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
Q07837-1	1.036	153	1.024	459.963	0.542	0.752	0.926	0.439	1.126	0.39	0.98	125,127,161,163,172,173,175,210,215,259,278,279,28 2,314,315,317,318,384,385,386,411,414,415,417,444, 446,447,448,449,450,451,456,477,479,498,499,502,50 6
Q07837-2	0.772	40	0.734	198.254	0.675	0.716	0.879	0.997	0.892	1.118	1.377	6,7,8,9,10,18,22,35,36,37,38,40,41,42,43,86
Q07837-3	0.913	98	0.942	268.226	0.769	0.573	0.715	0.105	1.02	0.103	1.061	18,19,20,21,22,111,112,113,114,115,116,117,119,120 ,153,156,157,158,201,203,204,205,206,307,309,371,3 77,379
Q07837-4	0.788	66	0.763	238.385	0.788	0.586	0.704	0.051	1.081	0.048	1.192	90,91,93,94,115,116,166,167,172,175,177,178,179,25 1,255,256,257,259,264,269,270,271,272,273,274,275, 277
Q07837-5	1.005	167	1.025	645.869	0.674	0.703	0.854	0.217	1.033	0.21	0.908	125,127,161,163,172,173,175,210,215,258,259,278,27 9,282,314,315,317,318,343,346,347,348,349,352,384, 386,387,388,392,411,414,415,444,446,447,448,449,45 0,451,452,456,479,480,486,488
Q07837-6	1.096	114	0.988	358.778	0.441	0.841	1.068	0.244	1.4	0.175	1.168	125,161,163,173,175,210,215,259,278,282,312,314,31 5,317,318,384,385,386,409,411,414,444,446,447,448, 449,450,502,506
Q07837-7	1.103	103	0.946	294.98	0.519	0.852	1.14	0.182	1.55	0.117	0.82	125,127,128,161,163,164,173,174,175,187,210,258,25 9,278,312,314,315,317,318,384,385,386,411,414,415, 444,446,447,448,449,450,506

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 Q07837-1_Q07837-1_6li9_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 Q07837-1_6li9_A_Q07837-2.pdb

3D view using mol* of Q07837-1_6li9_A_Q07837-3.pdb

3D view using mol* of Q07837-1_6li9_A_Q07837-4.pdb

3D view using mol* of Q07837-1_6li9_A_Q07837-5.pdb

3D view using mol* of Q07837-1_6li9_A_Q07837-6.pdb

3D view using mol* of Q07837-1_6li9_A_Q07837-7.pdb

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

3D view using mol* of Q07837-1_Q07837-2.pdb

3D view using mol* of Q07837-1_Q07837-3.pdb

3D view using mol* of Q07837-1_Q07837-4.pdb

3D view using mol* of Q07837-1_Q07837-5.pdb

3D view using mol* of Q07837-1_Q07837-6.pdb

3D view using mol* of Q07837-1_Q07837-7.pdb

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

./stats/secondary_structure/figure/Q07837-1_vs_Q07837-2.png