D-I-TASSER P02656

D-I-TASSER results for P02656

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

Summary of the Protein

Uniprot ID: P02656
Protein Name: Apolipoprotein C-III
Gene Name: APOC3

Input Sequence in FASTA format

>P02656 (99 residues)
MQPRVLLVVALLALLASARASEAEDASLLSFMQGYMKHATKTAKDALSSVQESQVAQQAR
GWVTDGFSSLKDYWSTVKDKFSEFWDLDPEVRPTSAVAA

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 AttentionPotential. 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	P02656-D1	1-99	99		MQPRVLLVVALLALLASARASEAEDASLLSFMQGYMKHATKTAKDALSSVQESQVAQQARGWVTDGFSSLKDYWSTVKDKFSEFWDLDPEVRPTSAVAA

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.5537

(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 AttentionPotential, 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	3ucaA	0.67	2.17	0.080	0.838	model1_3ucaA.pdb.gz
2	4ut1A	0.66	3.09	0.061	0.970	model1_4ut1A.pdb.gz
3	5xpdA	0.64	2.42	0.087	0.828	model1_5xpdA.pdb.gz
4	4jzbA	0.64	3.05	0.066	0.899	model1_4jzbA.pdb.gz
5	3rkoL1	0.64	3.17	0.098	0.929	model1_3rkoL1.pdb.gz
6	2ewgA	0.63	3.00	0.044	0.919	model1_2ewgA.pdb.gz
7	1v4jA	0.63	2.62	0.081	0.828	model1_1v4jA.pdb.gz
8	2f8zF	0.61	2.80	0.045	0.869	model1_2f8zF.pdb.gz
9	2dh4A	0.61	3.51	0.052	0.929	model1_2dh4A.pdb.gz
10	1rtrA1	0.61	2.65	0.046	0.828	model1_1rtrA1.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:0070653	1.00	high-density lipoprotein particle receptor binding
GO:0055102	1.00	lipase inhibitor activity
GO:0005543	1.00	phospholipid binding

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:0070328	1.00	triglyceride homeostasis
GO:0051005	1.00	negative regulation of lipoprotein lipase activity
GO:0042632	1.00	cholesterol homeostasis
GO:0034379	1.00	very-low-density lipoprotein particle assembly
GO:0010989	1.00	negative regulation of low-density lipoprotein particle clearance
GO:0010987	1.00	negative regulation of high-density lipoprotein particle clearance
GO:0010916	1.00	negative regulation of very-low-density lipoprotein particle clearance
GO:0010897	1.00	negative regulation of triglyceride catabolic process
GO:0006869	1.00	lipid transport
GO:0008152	0.53	metabolic process

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:0042627	1.00	chylomicron
GO:0034366	1.00	spherical high-density lipoprotein particle
GO:0034363	1.00	intermediate-density lipoprotein particle
GO:0034361	1.00	very-low-density lipoprotein particle
GO:0044464	0.70	cell part
GO:0044424	0.61	intracellular 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	0.066	1wcrA	0.516	4.13	0.057	0.869	2.7.1.69	NA
2	0.060	2j62A	0.555	3.21	0.047	0.859	3.2.1.52	NA
3	0.060	3lk5A	0.617	2.64	0.079	0.818	2.5.1.1	40,47
4	0.060	1biqB	0.544	4.08	0.104	0.929	1.17.4.1	NA
5	0.060	1s4bP	0.593	3.35	0.071	0.879	3.4.24.15	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	0.01	1few0	0.633	2.89	0.062	0.899	0.22	III	complex1.pdb.gz	29,32,35,39,42,43,46,49,53
2	0.01	3iczA	0.642	2.92	0.033	0.889	0.15	IPR	complex2.pdb.gz	10,13,33
3	0.01	3efqB	0.634	2.87	0.033	0.909	0.21	714	complex3.pdb.gz	10,11,14,15,18,19
4	0.01	3dygA	0.579	3.48	0.032	0.879	0.22	NI9	complex4.pdb.gz	11,12,15,19,31
5	0.01	3oabD	0.613	3.03	0.022	0.869	0.29	IPE	complex5.pdb.gz	19,31,35
6	0.01	3kroD	0.611	3.02	0.022	0.869	0.26	DST	complex6.pdb.gz	37,41,45
7	0.01	3krfA	0.611	2.97	0.022	0.869	0.27	PPV	complex7.pdb.gz	36,39,43
8	0.01	3ickA	0.642	2.92	0.033	0.889	0.16	M0N	complex8.pdb.gz	35,36,38,42
9	0.01	2f8zF	0.612	2.80	0.045	0.869	0.16	IPE	complex9.pdb.gz	10,33,42

	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, Chengxin Zhang, Yang Li, Robin Pearce, Eric W. Bell, Yang Zhang. Folding non-homology proteins by coupling deep-learning contact maps with I-TASSER assembly simulations. In preparation, 2020.