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:PLD1

Protein Summary

Gene summary

Gene name: PLD1
ASpdb.0 ID: 5337
	Gene
Gene symbol	PLD1
Gene ID	5337
Gene name	phospholipase D1
Synonyms	CVDD\|CVDP1
Cytomap	3q26.31
Type of gene	protein-coding
Description	phospholipase D1choline phosphatase 1phosphatidylcholine-hydrolyzing phospholipase D1phospholipase D1, phosphatidylcholine-specific
Modification date	20240403
UniProtAcc	Q13393

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

Partner	Gene	GO ID	GO term	PubMed ID
Gene	PLD1	GO:0004630	phospholipase D activity	25936805
Gene	PLD1	GO:0005768	endosome	14718562
Gene	PLD1	GO:0005794	Golgi apparatus	14718562
Gene	PLD1	GO:0016324	apical plasma membrane	22797597
Gene	PLD1	GO:0030139	endocytic vesicle	22797597
Gene	PLD1	GO:0031670	cellular response to nutrient	25936805
Gene	PLD1	GO:0098693	regulation of synaptic vesicle cycle	11752468
Gene	PLD1	GO:0098981	cholinergic synapse	11752468

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
Q13393-1	Q13393-1_6u8z_A.pdb	6U8Z	X-ray	1.8	A	336	1074

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

Q13393

PLD1

Q13393-1

Q13393-2

1074

1036

585

623

Substitution

SYFNHYRSHHNLIHGLKPHFKLFHPSSESEQGLTRPHAD

585

Q13393

PLD1

Q13393-1

Q13393-3

1074

597

514

597

Substitution

PAAMESMESLRLKDKNEPVQNLPIQKSIDDVDSKLKGIGKPRKFSKFSLYKQLHRHHLHDADSISSIDSTSSYFNHYRSHHNLI

IPGPSVVYRQVWESCMGKPDSGMERTTAISSSKTGFNLINLLLISLTGTPRPGCPGMTLPLQSTGRRLVMWHVTSSSAGTSQKL

514

597

Q13393

PLD1

Q13393-1

Q13393-3

1074

597

598

1074

Deletion

none

597

Q13393

PLD1

Q13393-1

Q13393-4

1074

971

962

971

Substitution

VVLGYLDDPS

SKMTPGVEDP

962

971

Q13393

PLD1

Q13393-1

Q13393-4

1074

971

972

1074

Deletion

none

971

Multiple sequence alignment of our canonical and alternatively spliced PLD1

Matched gene isoform IDs with Ensembl and RefSeq of our canonical and alternative spliced genes of PLD1

UniProt-id	ENSG	ENST	ENSP
Q13393-1	ENSG00000075651.17	ENST00000351298.9	ENSP00000342793.4
Q13393-2	ENSG00000075651.17	ENST00000356327.9	ENSP00000348681.5

UniProt-id	NM ID	NP ID
Q13393-1	NM_002662.4	NP_002653.1
Q13393-1	XM_005247533.2	XP_005247590.1
Q13393-2	XM_005247534.2	XP_005247591.1
Q13393-4	XM_011512897.1	XP_011511199.1

Amino acid sequences of our canonical and alternatively spliced PLD1

accession_id	Protein sequence
Q13393-1	MSLKNEPRVNTSALQKIAADMSNIIENLDTRELHFEGEEVDYDVSPSDPKIQEVYIPFSAIYNTQGFKEPNIQTYLSGCPIKAQVLEVER FTSTTRVPSINLYTIELTHGEFKWQVKRKFKHFQEFHRELLKYKAFIRIPIPTRRHTFRRQNVREEPREMPSLPRSSENMIREEQFLGRR KQLEDYLTKILKMPMYRNYHATTEFLDISQLSFIHDLGPKGIEGMIMKRSGGHRIPGLNCCGQGRACYRWSKRWLIVKDSFLLYMKPDSG AIAFVLLVDKEFKIKVGKKETETKYGIRIDNLSRTLILKCNSYRHARWWGGAIEEFIQKHGTNFLKDHRFGSYAAIQENALAKWYVNAKG YFEDVANAMEEANEEIFITDWWLSPEIFLKRPVVEGNRWRLDCILKRKAQQGVRIFIMLYKEVELALGINSEYTKRTLMRLHPNIKVMRH PDHVSSTVYLWAHHEKLVIIDQSVAFVGGIDLAYGRWDDNEHRLTDVGSVKRVTSGPSLGSLPPAAMESMESLRLKDKNEPVQNLPIQKS IDDVDSKLKGIGKPRKFSKFSLYKQLHRHHLHDADSISSIDSTSSYFNHYRSHHNLIHGLKPHFKLFHPSSESEQGLTRPHADTGSIRSL QTGVGELHGETRFWHGKDYCNFVFKDWVQLDKPFADFIDRYSTPRMPWHDIASAVHGKAARDVARHFIQRWNFTKIMKSKYRSLSYPFLL PKSQTTAHELRYQVPGSVHANVQLLRSAADWSAGIKYHEESIHAAYVHVIENSRHYIYIENQFFISCADDKVVFNKIGDAIAQRILKAHR ENQKYRVYVVIPLLPGFEGDISTGGGNALQAIMHFNYRTMCRGENSILGQLKAELGNQWINYISFCGLRTHAELEGNLVTELIYVHSKLL IADDNTVIIGSANINDRSMLGKRDSEMAVIVQDTETVPSVMDGKEYQAGRFARGLRLQCFRVVLGYLDDPSEDIQDPVSDKFFKEVWVST
Q13393-2	MSLKNEPRVNTSALQKIAADMSNIIENLDTRELHFEGEEVDYDVSPSDPKIQEVYIPFSAIYNTQGFKEPNIQTYLSGCPIKAQVLEVER FTSTTRVPSINLYTIELTHGEFKWQVKRKFKHFQEFHRELLKYKAFIRIPIPTRRHTFRRQNVREEPREMPSLPRSSENMIREEQFLGRR KQLEDYLTKILKMPMYRNYHATTEFLDISQLSFIHDLGPKGIEGMIMKRSGGHRIPGLNCCGQGRACYRWSKRWLIVKDSFLLYMKPDSG AIAFVLLVDKEFKIKVGKKETETKYGIRIDNLSRTLILKCNSYRHARWWGGAIEEFIQKHGTNFLKDHRFGSYAAIQENALAKWYVNAKG YFEDVANAMEEANEEIFITDWWLSPEIFLKRPVVEGNRWRLDCILKRKAQQGVRIFIMLYKEVELALGINSEYTKRTLMRLHPNIKVMRH PDHVSSTVYLWAHHEKLVIIDQSVAFVGGIDLAYGRWDDNEHRLTDVGSVKRVTSGPSLGSLPPAAMESMESLRLKDKNEPVQNLPIQKS IDDVDSKLKGIGKPRKFSKFSLYKQLHRHHLHDADSISSIDSTSNTGSIRSLQTGVGELHGETRFWHGKDYCNFVFKDWVQLDKPFADFI DRYSTPRMPWHDIASAVHGKAARDVARHFIQRWNFTKIMKSKYRSLSYPFLLPKSQTTAHELRYQVPGSVHANVQLLRSAADWSAGIKYH EESIHAAYVHVIENSRHYIYIENQFFISCADDKVVFNKIGDAIAQRILKAHRENQKYRVYVVIPLLPGFEGDISTGGGNALQAIMHFNYR TMCRGENSILGQLKAELGNQWINYISFCGLRTHAELEGNLVTELIYVHSKLLIADDNTVIIGSANINDRSMLGKRDSEMAVIVQDTETVP SVMDGKEYQAGRFARGLRLQCFRVVLGYLDDPSEDIQDPVSDKFFKEVWVSTAARNATIYDKVFRCLPNDEVHNLIQLRDFINKPVLAKE
Q13393-3	MSLKNEPRVNTSALQKIAADMSNIIENLDTRELHFEGEEVDYDVSPSDPKIQEVYIPFSAIYNTQGFKEPNIQTYLSGCPIKAQVLEVER FTSTTRVPSINLYTIELTHGEFKWQVKRKFKHFQEFHRELLKYKAFIRIPIPTRRHTFRRQNVREEPREMPSLPRSSENMIREEQFLGRR KQLEDYLTKILKMPMYRNYHATTEFLDISQLSFIHDLGPKGIEGMIMKRSGGHRIPGLNCCGQGRACYRWSKRWLIVKDSFLLYMKPDSG AIAFVLLVDKEFKIKVGKKETETKYGIRIDNLSRTLILKCNSYRHARWWGGAIEEFIQKHGTNFLKDHRFGSYAAIQENALAKWYVNAKG YFEDVANAMEEANEEIFITDWWLSPEIFLKRPVVEGNRWRLDCILKRKAQQGVRIFIMLYKEVELALGINSEYTKRTLMRLHPNIKVMRH PDHVSSTVYLWAHHEKLVIIDQSVAFVGGIDLAYGRWDDNEHRLTDVGSVKRVTSGPSLGSLPIPGPSVVYRQVWESCMGKPDSGMERTT
Q13393-4	MSLKNEPRVNTSALQKIAADMSNIIENLDTRELHFEGEEVDYDVSPSDPKIQEVYIPFSAIYNTQGFKEPNIQTYLSGCPIKAQVLEVER FTSTTRVPSINLYTIELTHGEFKWQVKRKFKHFQEFHRELLKYKAFIRIPIPTRRHTFRRQNVREEPREMPSLPRSSENMIREEQFLGRR KQLEDYLTKILKMPMYRNYHATTEFLDISQLSFIHDLGPKGIEGMIMKRSGGHRIPGLNCCGQGRACYRWSKRWLIVKDSFLLYMKPDSG AIAFVLLVDKEFKIKVGKKETETKYGIRIDNLSRTLILKCNSYRHARWWGGAIEEFIQKHGTNFLKDHRFGSYAAIQENALAKWYVNAKG YFEDVANAMEEANEEIFITDWWLSPEIFLKRPVVEGNRWRLDCILKRKAQQGVRIFIMLYKEVELALGINSEYTKRTLMRLHPNIKVMRH PDHVSSTVYLWAHHEKLVIIDQSVAFVGGIDLAYGRWDDNEHRLTDVGSVKRVTSGPSLGSLPPAAMESMESLRLKDKNEPVQNLPIQKS IDDVDSKLKGIGKPRKFSKFSLYKQLHRHHLHDADSISSIDSTSSYFNHYRSHHNLIHGLKPHFKLFHPSSESEQGLTRPHADTGSIRSL QTGVGELHGETRFWHGKDYCNFVFKDWVQLDKPFADFIDRYSTPRMPWHDIASAVHGKAARDVARHFIQRWNFTKIMKSKYRSLSYPFLL PKSQTTAHELRYQVPGSVHANVQLLRSAADWSAGIKYHEESIHAAYVHVIENSRHYIYIENQFFISCADDKVVFNKIGDAIAQRILKAHR ENQKYRVYVVIPLLPGFEGDISTGGGNALQAIMHFNYRTMCRGENSILGQLKAELGNQWINYISFCGLRTHAELEGNLVTELIYVHSKLL

Protein Functional Features

Main function of this protein. (from UniProt)

PLD1 (go to UniProt):Q13393

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
Q13393	Domain	891	918	Note=PLD phosphodiesterase 2;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00153	Type=Deletion;Start=598;End=1074
Q13393	Region	463	928	Note=Catalytic	Type=Substitution;Start=585;End=623
Q13393	Region	463	928	Note=Catalytic	Type=Substitution;Start=514;End=597
Q13393	Region	463	928	Note=Catalytic	Type=Deletion;Start=598;End=1074

Gene Isoform Structures and Expression Levels for PLD1

Gene structures of our canonical and alternative spliced genes of PLD1
* 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 Q13393-1

3D view using mol* of Q13393-2

3D view using mol* of Q13393-3

3D view using mol* of Q13393-4

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 Q13393-1

pLDDT distribution across the protein length of Q13393-2

pLDDT distribution across the protein length of Q13393-3

pLDDT distribution across the protein length of Q13393-4

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 Q13393-1

Ramachandran plot of Q13393-2

Ramachandran plot of Q13393-3

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
Q13393-1	1.056	177	1.1	490.147	0.537	0.725	0.929	0.963	0.843	1.143	0.625	89,102,116,117,118,119,122,125,126,129,200,201,204 ,205,207,222,223,224,225,226,227,252,254,309,310,3 11,312,314,315,318,319
Q13393-2	1.081	148	1.065	242.158	0.46	0.819	1.142	0.905	1.125	0.805	0.604	233,234,235,274,275,276,277,278,279,280,301,302,30 3,334,336,337,338,340,341,342,343,657,661,664,665, 668,669,708,715,716,717,719,720,721,722,723
Q13393-3	1.053	202	1.1	501.809	0.541	0.715	0.922	0.836	0.824	1.015	0.673	89,91,92,93,97,98,99,100,102,117,118,119,122,125,1 26,129,201,204,205,207,223,224,225,226,227,252,254 ,295,309,310,311,312,313,314,315,318,319
Q13393-4	1.034	430	1.076	1129.156	0.561	0.699	0.914	0.919	0.868	1.058	0.927	21,24,25,27,28,29,31,32,66,67,68,69,70,89,91,100,1 02,104,111,112,113,114,115,116,117,118,119,122,125 ,126,128,129,132,133,135,136,139,141,199,200,201,2 03,204,205,207,215,218,219,220,221,222,223,224,225 ,226,227,252,254,267,268,269,309,310,311,312,313,3 14,315,317,318,319,321,322,325,326,329,330,725,726 ,728

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 Q13393-1_Q13393-1_6u8z_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 Q13393-1_6u8z_A_Q13393-2.pdb

3D view using mol* of Q13393-1_6u8z_A_Q13393-3.pdb

3D view using mol* of Q13393-1_6u8z_A_Q13393-4.pdb

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

3D view using mol* of Q13393-1_Q13393-2.pdb

3D view using mol* of Q13393-1_Q13393-3.pdb

3D view using mol* of Q13393-1_Q13393-4.pdb

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

./stats/secondary_structure/figure/Q13393-1_vs_Q13393-2.png

./stats/secondary_structure/figure/Q13393-1_vs_Q13393-3.png

./stats/secondary_structure/figure/Q13393-1_vs_Q13393-4.png

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

./stats/relative_asa/Q13393-1_vs_Q13393-2.png

./stats/relative_asa/Q13393-1_vs_Q13393-3.png

./stats/relative_asa/Q13393-1_vs_Q13393-4.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 PLD1

Drugs targeting this gene/protein.
(DrugBank)

UniProt accession	Gene name	DrugBank ID	Drug name	Drug group	Actions
Q13393	PLD1	DB05301	LAX-101	investigational
Q13393	PLD1	DB14006	Choline salicylate	approved, nutraceutical	product of
Q13393	PLD1	DB00122	Choline	approved, nutraceutical	product of

Related Diseases to PLD1

Previous studies relating to the alternative splicing of PLD1 and disease information from the MeSH term (PubMed)

Gene

PMID

Title

Abstract

MeSH ID

MeSH term

Clinically important variants in PLD1

(ClinVar, 04/20/2024)

accession_id

uniprot_id

gene_name

Type

Variant

Clinical_significance