D-I-TASSER P13637

D-I-TASSER results for P13637

[Click result.zip to download all results on this page]

Summary of the Protein

Uniprot ID: P13637
Protein Name: Sodium/potassium-transporting ATPase subunit alpha-3
Gene Name: ATP1A3

Input Sequence in FASTA format

>P13637 (1013 residues)
MGDKKDDKDSPKKNKGKERRDLDDLKKEVAMTEHKMSVEEVCRKYNTDCVQGLTHSKAQE
ILARDGPNALTPPPTTPEWVKFCRQLFGGFSILLWIGAILCFLAYGIQAGTEDDPSGDNL
YLGIVLAAVVIITGCFSYYQEAKSSKIMESFKNMVPQQALVIREGEKMQVNAEEVVVGDL
VEIKGGDRVPADLRIISAHGCKVDNSSLTGESEPQTRSPDCTHDNPLETRNITFFSTNCV
EGTARGVVVATGDRTVMGRIATLASGLEVGKTPIAIEIEHFIQLITGVAVFLGVSFFILS
LILGYTWLEAVIFLIGIIVANVPEGLLATVTVCLTLTAKRMARKNCLVKNLEAVETLGST
STICSDKTGTLTQNRMTVAHMWFDNQIHEADTTEDQSGTSFDKSSHTWVALSHIAGLCNR
AVFKGGQDNIPVLKRDVAGDASESALLKCIELSSGSVKLMRERNKKVAEIPFNSTNKYQL
SIHETEDPNDNRYLLVMKGAPERILDRCSTILLQGKEQPLDEEMKEAFQNAYLELGGLGE
RVLGFCHYYLPEEQFPKGFAFDCDDVNFTTDNLCFVGLMSMIDPPRAAVPDAVGKCRSAG
IKVIMVTGDHPITAKAIAKGVGIISEGNETVEDIAARLNIPVSQVNPRDAKACVIHGTDL
KDFTSEQIDEILQNHTEIVFARTSPQQKLIIVEGCQRQGAIVAVTGDGVNDSPALKKADI
GVAMGIAGSDVSKQAADMILLDDNFASIVTGVEEGRLIFDNLKKSIAYTLTSNIPEITPF
LLFIMANIPLPLGTITILCIDLGTDMVPAISLAYEAAESDIMKRQPRNPRTDKLVNERLI
SMAYGQIGMIQALGGFFSYFVILAENGFLPGNLVGIRLNWDDRTVNDLEDSYGQQWTYEQ
RKVVEFTCHTAFFVSIVVVQWADLIICKTRRNSVFQQGMKNKILIFGLFEETALAAFLSY
CPGMDVALRMYPLKPSWWFCAFPYSFLIFVYDEIRKLILRRNPGGWVEKETYY

Predicted Contact and Distance Map Used in D-I-TASSER simulation

Contact Map

Distance Map

D-I-TASSER simulation is guided by the consensus contact map (left figure) and distance map (right figure) derived based on confidence scores of DeepPotential. In the contact, distance map and hydrogen bond networks, the axes mark the residue index along the sequence. For the contact map, each dot represents a residue pair with predicted contact, while for the distance map and hydrogen bond network, a color scale represents a distance of 1-20+ angstroms or a angle of 0-180 degree.

Information of Domain

No. of Domain	Domain	Domain Boundary	Length of Domain	Models of Domain	Sequence
1	P13637-D1	1-71,158-252	166		MGDKKDDKDSPKKNKGKERRDLDDLKKEVAMTEHKMSVEEVCRKYNTDCVQGLTHSKAQEILARDGPNALTQALVIREGEKMQVNAEEVVVGDLVEIKGGDRVPADLRIISAHGCKVDNSSLTGESEPQTRSPDCTHDNPLETRNITFFSTNCVEGTARGVVVATG
2	P13637-D2	72-157,253-375,583-1013	640		PPPTTPEWVKFCRQLFGGFSILLWIGAILCFLAYGIQAGTEDDPSGDNLYLGIVLAAVVIITGCFSYYQEAKSSKIMESFKNMVPQDRTVMGRIATLASGLEVGKTPIAIEIEHFIQLITGVAVFLGVSFFILSLILGYTWLEAVIFLIGIIVANVPEGLLATVTVCLTLTAKRMARKNCLVKNLEAVETLGSTSTICSDKTGTLTQNRDPPRAAVPDAVGKCRSAGIKVIMVTGDHPITAKAIAKGVGIISEGNETVEDIAARLNIPVSQVNPRDAKACVIHGTDLKDFTSEQIDEILQNHTEIVFARTSPQQKLIIVEGCQRQGAIVAVTGDGVNDSPALKKADIGVAMGIAGSDVSKQAADMILLDDNFASIVTGVEEGRLIFDNLKKSIAYTLTSNIPEITPFLLFIMANIPLPLGTITILCIDLGTDMVPAISLAYEAAESDIMKRQPRNPRTDKLVNERLISMAYGQIGMIQALGGFFSYFVILAENGFLPGNLVGIRLNWDDRTVNDLEDSYGQQWTYEQRKVVEFTCHTAFFVSIVVVQWADLIICKTRRNSVFQQGMKNKILIFGLFEETALAAFLSYCPGMDVALRMYPLKPSWWFCAFPYSFLIFVYDEIRKLILRRNPGGWVEKETYY
3	P13637-D3	376-582	207		MTVAHMWFDNQIHEADTTEDQSGTSFDKSSHTWVALSHIAGLCNRAVFKGGQDNIPVLKRDVAGDASESALLKCIELSSGSVKLMRERNKKVAEIPFNSTNKYQLSIHETEDPNDNRYLLVMKGAPERILDRCSTILLQGKEQPLDEEMKEAFQNAYLELGGLGERVLGFCHYYLPEEQFPKGFAFDCDDVNFTTDNLCFVGLMSMI

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.742

(a)

D-I-TASSER simulations generate a large ensemble of structural conformations, i.e. decoys. These decoys are clustered by SPICKER based on pairwise structure similarity to report up to five final models from the five largest clusters. Models are ranked in descending order of cluster size. If the simulations converge well, it is possible to have less than 5 models generated, which is usually an indication of good model quality.

(b)

The model confidence is quantitatified by estimated TM-score (eTM-score), calculated based on significance of threading template alignments, contact map satisfaction rate, mean absolute error between distance of model and distance of DeepPotential, and convergence of D-I-TASSER simulations. eTM-score is typically in the range of [0, 1], with higher eTM-score signifies higher model confidence.

Proteins with similar structure

Top 10 structural analogs in PDB (as identified by TM-align)

Rank	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	Download Alignment
1	3kdpA	0.90	3.34	0.834	0.981	model1_3kdpA.pdb.gz
2	8d3yA	0.90	3.03	0.972	0.965	model1_8d3yA.pdb.gz
3	7x20A	0.89	3.41	0.626	0.967	model1_7x20A.pdb.gz
4	7w47A	0.89	3.34	0.621	0.965	model1_7w47A.pdb.gz
5	7n70A	0.78	4.60	0.176	0.890	model1_7n70A.pdb.gz
6	6zhfA	0.78	3.40	0.297	0.852	model1_6zhfA.pdb.gz
7	7op1A	0.77	4.87	0.160	0.899	model1_7op1A.pdb.gz
8	6lcpA	0.72	5.35	0.144	0.858	model1_6lcpA.pdb.gz
9	7drxA	0.71	5.42	0.148	0.854	model1_7drxA.pdb.gz
10	7ky5A	0.71	5.64	0.143	0.864	model1_7ky5A.pdb.gz

(a)	Query structure is shown in cartoon, while the structural analog is displayed using backbone trace.
(b)	Ranking of proteins is based on TM-score of the structural alignment between the query structure and known structures in the PDB library.
(c)	RMSD^a is the RMSD between residues that are structurally aligned by TM-align.
(d)	IDEN^a is the percentage sequence identity in the structurally aligned region.
(e)	Cov. represents the coverage of the alignment by TM-align and is equal to the number of structurally aligned residues divided by length of the query protein.

Predicted Gene Ontology (GO) Terms

Molecular Function (MF)

GO term	Cscore^GO	Name
GO:0022892	1.00	substrate-specific transporter activity
GO:0003824	1.00	catalytic activity
GO:0043492	0.99	ATPase activity, coupled to movement of substances
GO:0022891	0.94	substrate-specific transmembrane transporter activity
GO:0022804	0.93	active transmembrane transporter activity
GO:0008324	0.93	cation transmembrane transporter activity
GO:0019829	0.92	cation-transporting ATPase activity
GO:0022890	0.78	inorganic cation transmembrane transporter activity
GO:0015662	0.75	ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism
GO:0046873	0.71	metal ion transmembrane transporter activity

Download full result of the above consensus prediction.

Click the graph to show a high resolution version.

(a)

Cscore^GO is the confidence score of predicted GO terms. Cscore^GO values range in between [0-1]; where a higher value indicates a better confidence in predicting the function using the template.

(b)

The graph shows the predicted terms within the Gene Ontology hierachy for Molecular Function. Confidently predicted terms are color coded by Cscore^GO:

[0.4,0.5)

[0.5,0.6)

[0.6,0.7)

[0.7,0.8)

[0.8,0.9)

[0.9,1.0]

Biological Process (BP)

GO term	Cscore^GO	Name
GO:0044699	0.93	single-organism process
GO:0009987	0.92	cellular process
GO:0065007	0.90	biological regulation
GO:0044763	0.87	single-organism cellular process
GO:0065008	0.83	regulation of biological quality
GO:0098771	0.80	inorganic ion homeostasis
GO:0030003	0.80	cellular cation homeostasis
GO:0006875	0.71	cellular metal ion homeostasis
GO:0051234	0.67	establishment of localization
GO:0006810	0.66	transport
GO:0006811	0.57	ion transport
GO:0006812	0.55	cation transport
GO:0055085	0.54	transmembrane transport

Download full result of the above consensus prediction.

Click the graph to show a high resolution version.

(a)

Cscore^GO is the confidence score of predicted GO terms. Cscore^GO values range in between [0-1]; where a higher value indicates a better confidence in predicting the function using the template.

(b)

The graph shows the predicted terms within the Gene Ontology hierachy for Biological Process. Confidently predicted terms are color coded by Cscore^GO:

[0.4,0.5)

[0.5,0.6)

[0.6,0.7)

[0.7,0.8)

[0.8,0.9)

[0.9,1.0]

Cellular Component (CC)

GO term	Cscore^GO	Name
GO:0044464	0.99	cell part
GO:0044424	0.96	intracellular part
GO:0044425	0.91	membrane part
GO:0016021	0.88	integral component of membrane
GO:0044459	0.85	plasma membrane part
GO:0043226	0.83	organelle
GO:0043231	0.82	intracellular membrane-bounded organelle
GO:0005887	0.80	integral component of plasma membrane
GO:0016020	0.55	membrane
GO:0044444	0.52	cytoplasmic part

Download full result of the above consensus prediction.

Click the graph to show a high resolution version.

(a)

Cscore^GO is the confidence score of predicted GO terms. Cscore^GO values range in between [0-1]; where a higher value indicates a better confidence in predicting the function using the template.

(b)

The graph shows the predicted terms within the Gene Ontology hierachy for Cellular Component. Confidently predicted terms are color coded by Cscore^GO:

[0.4,0.5)

[0.5,0.6)

[0.6,0.7)

[0.7,0.8)

[0.8,0.9)

[0.9,1.0]

Predicted Enzyme Commission (EC) Numbers

Top 5 enzyme homologs in PDB

Rank	Cscore^EC	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	EC Number	Predicted Active Site Residues
1	0.483	3b8cA	0.592	6.13	0.134	0.741	3.6.3.6	366
2	0.453	1eulA	0.589	6.92	0.218	0.779	3.6.3.8	366
3	0.223	3ixzA	0.878	3.72	0.583	0.971	3.6.3.10	366
4	0.145	3b8eA	0.892	3.45	0.796	0.975	3.6.3.9	366
5	0.060	2zxqA	0.251	9.02	0.038	0.392	3.2.1.97	NA

	Click on the radio buttons to visualize predicted active site residues.
(a)	Cscore^EC is the confidence score for the Enzyme Commission (EC) number prediction. Cscore^EC values range in between [0-1]; where a higher score indicates a more reliable EC number prediction.
(b)	TM-score is a measure of global structural similarity between query and template protein.
(c)	RMSD^a is the RMSD between residues that are structurally aligned by TM-align.
(d)	IDEN^a is the percentage sequence identity in the structurally aligned region.
(e)	Cov. represents the coverage of global structural alignment and is equal to the number of structurally aligned residues divided by length of the query protein.

Predicted Ligand Binding Sites

Template proteins with similar binding site:

Rank	Cscore^LB	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	BS-score	Lig. Name	Download Complex	Predicted binding site residues
1	0.37	3kdpA	0.902	3.34	0.834	0.981	0.23	MF4	complex1.pdb.gz	54,164,178,179,180
2	0.18	3fpbA	0.828	3.79	0.282	0.920	0.25	CZA	complex2.pdb.gz	69,249,251,256
3	0.17	3ar3A	0.787	4.53	0.270	0.909	0.34	PTY	complex3.pdb.gz	67,255,258
4	0.17	2easA	0.795	4.46	0.264	0.913	0.27	CZA	complex4.pdb.gz	66,189,190,249,250,251,256
5	0.16	2agvB	0.784	4.65	0.268	0.911	0.17	BHQ	complex5.pdb.gz	68,70,257
6	0.13	3a3yA	0.883	3.66	0.816	0.974	0.20	MF4	complex6.pdb.gz	45,163,178
7	0.09	3fpsA	0.792	4.53	0.263	0.912	0.25	CZA	complex7.pdb.gz	65,250,251
8	0.06	1t5sA	0.652	5.93	0.223	0.800	0.11	ACP	complex8.pdb.gz	62,161,163,191,249,257

	Click on the radio buttons to visualize predicted binding site and residues.
(a)	Cscore^LB is the confidence score of predicted binding site. Cscore^LB values range in between [0-1]; where a higher score indicates a more reliable ligand-binding site prediction.
(b)	BS-score is a measure of local similarity (sequence & structure) between template binding site and predicted binding site in the query structure. Based on large scale benchmarking analysis, we have observed that a BS-score >1 reflects a significant local match between the predicted and template binding site.
(c)	TM-score is a measure of global structural similarity between query and template protein.
(d)	RMSD^a the RMSD between residues that are structurally aligned by TM-align.
(e)	IDEN^a is the percentage sequence identity in the structurally aligned region.
(f)	Cov. represents the coverage of global structural alignment and is equal to the number of structurally aligned residues divided by length of the query protein.

[Click result.zip to download all results on this page]

References:
1.	Wei Zheng, Qiqige Wuyun, Yang Li, Quancheng Liu, Xiaogen Zhou, Yiheng Zhu, P. Lydia Freddolino, Yang Zhang. Integrating deep learning potentials with I-TASSER for single- and multi-domain protein structure prediction. Submitted. 2023.