D-I-TASSER P02649

D-I-TASSER results for P02649

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

Summary of the Protein

Uniprot ID: P02649
Protein Name: Apolipoprotein E
Gene Name: APOE

Input Sequence in FASTA format

>P02649 (317 residues)
MKVLWAALLVTFLAGCQAKVEQAVETEPEPELRQQTEWQSGQRWELALGRFWDYLRWVQT
LSEQVQEELLSSQVTQELRALMDETMKELKAYKSELEEQLTPVAEETRARLSKELQAAQA
RLGADMEDVCGRLVQYRGEVQAMLGQSTEELRVRLASHLRKLRKRLLRDADDLQKRLAVY
QAGAREGAERGLSAIRERLGPLVEQGRVRAATVGSLAGQPLQERAQAWGERLRARMEEMG
SRTRDRLDEVKEQVAEVRAKLEEQAQQIRLQAEAFQARLKSWFEPLVEDMQRQWAGLVEK
VQAAVGTSAAPVPSDNH

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	P02649-D1	1-317	317		MKVLWAALLVTFLAGCQAKVEQAVETEPEPELRQQTEWQSGQRWELALGRFWDYLRWVQTLSEQVQEELLSSQVTQELRALMDETMKELKAYKSELEEQLTPVAEETRARLSKELQAAQARLGADMEDVCGRLVQYRGEVQAMLGQSTEELRVRLASHLRKLRKRLLRDADDLQKRLAVYQAGAREGAERGLSAIRERLGPLVEQGRVRAATVGSLAGQPLQERAQAWGERLRARMEEMGSRTRDRLDEVKEQVAEVRAKLEEQAQQIRLQAEAFQARLKSWFEPLVEDMQRQWAGLVEKVQAAVGTSAAPVPSDNH

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.4263

(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	2l7bA	0.91	1.29	0.983	0.943	model1_2l7bA.pdb.gz
2	6z16A	0.46	6.29	0.059	0.741	model1_6z16A.pdb.gz
3	2kc3A	0.46	2.50	0.822	0.511	model1_2kc3A.pdb.gz
4	3rkoL	0.45	5.95	0.050	0.704	model1_3rkoL.pdb.gz
5	1xmeA	0.44	6.41	0.045	0.729	model1_1xmeA.pdb.gz
6	3nz4A	0.44	5.19	0.052	0.640	model1_3nz4A.pdb.gz
7	5doqA	0.44	5.46	0.068	0.637	model1_5doqA.pdb.gz
8	1y2mB	0.42	5.77	0.067	0.656	model1_1y2mB.pdb.gz
9	2nyfA2	0.40	5.28	0.068	0.587	model1_2nyfA2.pdb.gz
10	3o0rB	0.40	4.91	0.030	0.549	model1_3o0rB.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:0097159	0.75	organic cyclic compound binding
GO:0042277	0.73	peptide binding
GO:0036094	0.73	small molecule binding
GO:0030234	0.72	enzyme regulator activity
GO:0022892	0.72	substrate-specific transporter activity
GO:0008289	0.72	lipid binding
GO:0001540	0.72	beta-amyloid binding
GO:0060228	0.71	phosphatidylcholine-sterol O-acyltransferase activator activity
GO:0017127	0.71	cholesterol transporter activity
GO:0015485	0.71	cholesterol binding
GO:0005102	0.55	receptor binding
GO:0070325	0.50	lipoprotein particle receptor 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:0051239	1.00	regulation of multicellular organismal process
GO:0046889	1.00	positive regulation of lipid biosynthetic process
GO:0044255	1.00	cellular lipid metabolic process
GO:0044248	1.00	cellular catabolic process
GO:0043691	1.00	reverse cholesterol transport
GO:0043085	1.00	positive regulation of catalytic activity
GO:0042632	1.00	cholesterol homeostasis
GO:0042157	1.00	lipoprotein metabolic process
GO:0034380	1.00	high-density lipoprotein particle assembly
GO:0034372	1.00	very-low-density lipoprotein particle remodeling
GO:0033700	1.00	phospholipid efflux
GO:0033344	1.00	cholesterol efflux
GO:0032374	1.00	regulation of cholesterol transport
GO:0031102	1.00	neuron projection regeneration
GO:0016042	1.00	lipid catabolic process
GO:0010873	1.00	positive regulation of cholesterol esterification
GO:0008203	1.00	cholesterol metabolic process
GO:0019433	0.99	triglyceride catabolic process
GO:0006695	0.88	cholesterol biosynthetic process
GO:0048519	0.67	negative regulation of biological process
GO:0048523	0.66	negative regulation of cellular process
GO:2000026	0.62	regulation of multicellular organismal development
GO:0051128	0.62	regulation of cellular component organization
GO:0045595	0.62	regulation of cell differentiation
GO:0022603	0.62	regulation of anatomical structure morphogenesis
GO:0010769	0.61	regulation of cell morphogenesis involved in differentiation
GO:1900221	0.60	regulation of beta-amyloid clearance
GO:0051000	0.60	positive regulation of nitric-oxide synthase activity
GO:0043524	0.60	negative regulation of neuron apoptotic process
GO:0042159	0.60	lipoprotein catabolic process
GO:0030516	0.60	regulation of axon extension
GO:0006707	0.60	cholesterol catabolic process
GO:0031326	0.56	regulation of cellular biosynthetic process
GO:0031328	0.55	positive regulation of cellular biosynthetic process
GO:0031331	0.53	positive regulation of cellular catabolic 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:0044421	0.99	extracellular region part
GO:0032991	0.99	macromolecular complex
GO:0072562	0.98	blood microparticle
GO:0042627	0.98	chylomicron
GO:0034364	0.98	high-density lipoprotein particle
GO:0044464	0.72	cell part
GO:0034385	0.63	triglyceride-rich lipoprotein particle
GO:0044424	0.61	intracellular part
GO:0034363	0.59	intermediate-density lipoprotein particle

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	0.060	1b8fA	0.409	5.31	0.061	0.603	4.3.1.3	NA
2	0.060	3dy5A	0.437	5.60	0.056	0.666	1.13.11.40 4.2.1.92	NA
3	0.060	1fftA	0.416	6.56	0.033	0.729	1.10.3.-	NA
4	0.060	1f1hL	0.401	5.83	0.037	0.609	6.3.1.2	198
5	0.060	3b8cB	0.423	5.98	0.043	0.656	3.6.3.6	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:

Click to view	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	2agvA	0.396	6.45	0.042	0.650	0.70	PTY	complex1.pdb.gz	76,130,134,137,138

	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.