D-I-TASSER P20783

D-I-TASSER results for P20783

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

Summary of the Protein

Uniprot ID: P20783
Protein Name: Neurotrophin-3
Gene Name: NTF3

Input Sequence in FASTA format

>P20783 (257 residues)
MSILFYVIFLAYLRGIQGNNMDQRSLPEDSLNSLIIKLIQADILKNKLSKQMVDVKENYQ
STLPKAEAPREPERGGPAKSAFQPVIAMDTELLRQQRRYNSPRVLLSDSTPLEPPPLYLM
EDYVGSPVVANRTSRRKRYAEHKSHRGEYSVCDSESLWVTDKSSAIDIRGHQVTVLGEIK
TGNSPVKQYFYETRCKEARPVKNGCRGIDDKHWNSQCKTSQTYVRALTSENNKLVGWRWI
RIDTSCVCALSRKIGRT

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	P20783-D1	1-257	257		MSILFYVIFLAYLRGIQGNNMDQRSLPEDSLNSLIIKLIQADILKNKLSKQMVDVKENYQSTLPKAEAPREPERGGPAKSAFQPVIAMDTELLRQQRRYNSPRVLLSDSTPLEPPPLYLMEDYVGSPVVANRTSRRKRYAEHKSHRGEYSVCDSESLWVTDKSSAIDIRGHQVTVLGEIKTGNSPVKQYFYETRCKEARPVKNGCRGIDDKHWNSQCKTSQTYVRALTSENNKLVGWRWIRIDTSCVCALSRKIGRT

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.601

(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	5i6fA	0.44	6.16	0.043	0.755	model1_5i6fA.pdb.gz
2	6um1A	0.41	6.25	0.037	0.720	model1_6um1A.pdb.gz
3	6bfiA	0.41	5.49	0.038	0.638	model1_6bfiA.pdb.gz
4	7bvcA	0.40	6.02	0.050	0.669	model1_7bvcA.pdb.gz
5	1ej6A	0.40	6.05	0.035	0.661	model1_1ej6A.pdb.gz
6	7dxjA	0.40	5.74	0.026	0.658	model1_7dxjA.pdb.gz
7	1i8qA	0.40	5.99	0.023	0.661	model1_1i8qA.pdb.gz
8	7kbtA	0.40	5.83	0.037	0.661	model1_7kbtA.pdb.gz
9	3eifA	0.39	5.88	0.053	0.673	model1_3eifA.pdb.gz
10	6d6vA	0.39	5.43	0.053	0.623	model1_6d6vA.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:0005102	0.75	receptor binding
GO:0008083	0.70	growth factor activity
GO:0005165	0.69	neurotrophin 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:0050794	0.96	regulation of cellular process
GO:0044699	0.96	single-organism process
GO:0032502	0.96	developmental process
GO:0009987	0.96	cellular process
GO:0044763	0.95	single-organism cellular process
GO:0048523	0.94	negative regulation of cellular process
GO:0044767	0.94	single-organism developmental process
GO:0048869	0.93	cellular developmental process
GO:0043069	0.93	negative regulation of programmed cell death
GO:0007165	0.93	signal transduction
GO:0045664	0.92	regulation of neuron differentiation
GO:0043524	0.92	negative regulation of neuron apoptotic process
GO:0007166	0.92	cell surface receptor signaling pathway
GO:0007169	0.91	transmembrane receptor protein tyrosine kinase signaling pathway
GO:0016043	0.89	cellular component organization
GO:0030030	0.87	cell projection organization
GO:0007154	0.87	cell communication
GO:0048812	0.86	neuron projection morphogenesis
GO:0007267	0.86	cell-cell signaling

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	1.00	cell part
GO:0044424	0.99	intracellular part
GO:0043231	0.98	intracellular membrane-bounded organelle
GO:0044444	0.96	cytoplasmic part
GO:0005576	0.96	extracellular region
GO:0016023	0.94	cytoplasmic, membrane-bounded vesicle

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	2e9bA	0.367	5.82	0.053	0.611	3.2.1.41	211
2	0.060	1f1sA	0.366	5.85	0.037	0.611	4.2.2.1	NA
3	0.060	3ffzA	0.364	6.31	0.055	0.650	3.4.24.69	NA
4	0.060	3b8eC	0.366	6.31	0.040	0.650	3.6.3.9	207
5	0.060	2vkzG	0.341	6.92	0.024	0.654	2.3.1.38 3.1.2.14	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	2y0pA	0.304	6.27	0.029	0.537	0.21	TD7	complex1.pdb.gz	146,148,207
2	0.01	1xkhA	0.320	6.31	0.038	0.572	0.19	PVE	complex2.pdb.gz	206,214,215
3	0.01	1g9aA	0.369	5.75	0.036	0.595	0.15	BAB	complex3.pdb.gz	146,151,152,196,197,218,219
4	0.01	2nm1A	0.239	6.29	0.024	0.420	0.17	III	complex4.pdb.gz	171,172,173,174,177
5	0.01	2w16B	0.333	5.97	0.034	0.556	0.15	PVE	complex5.pdb.gz	208,210,213
6	0.01	2e8zA	0.378	5.91	0.033	0.650	0.17	GLC	complex6.pdb.gz	148,204,214
7	0.01	1i1eA	0.366	5.72	0.036	0.591	0.40	DM2	complex7.pdb.gz	153,154,205,207
8	0.01	3c46A	0.347	6.38	0.065	0.626	0.35	2HP	complex8.pdb.gz	206,207,208,209
9	0.01	2xt6A	0.365	6.00	0.040	0.623	0.15	TPP	complex9.pdb.gz	147,148,149,152,153

	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.