D-I-TASSER P10747

D-I-TASSER results for P10747

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

Summary of the Protein

Uniprot ID: P10747
Protein Name: T-cell-specific surface glycoprotein CD28
Gene Name: CD28

Input Sequence in FASTA format

>P10747 (220 residues)
MLRLLLALNLFPSIQVTGNKILVKQSPMLVAYDNAVNLSCKYSYNLFSREFRASLHKGLD
SAVEVCVVYGNYSQQLQVYSKTGFNCDGKLGNESVTFYLQNLYVNQTDIYFCKIEVMYPP
PYLDNEKSNGTIIHVKGKHLCPSPLFPGPSKPFWVLVVVGGVLACYSLLVTVAFIIFWVR
SKRSRLLHSDYMNMTPRRPGPTRKHYQPYAPPRDFAAYRS

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	P10747-D1	1-220	220		MLRLLLALNLFPSIQVTGNKILVKQSPMLVAYDNAVNLSCKYSYNLFSREFRASLHKGLDSAVEVCVVYGNYSQQLQVYSKTGFNCDGKLGNESVTFYLQNLYVNQTDIYFCKIEVMYPPPYLDNEKSNGTIIHVKGKHLCPSPLFPGPSKPFWVLVVVGGVLACYSLLVTVAFIIFWVRSKRSRLLHSDYMNMTPRRPGPTRKHYQPYAPPRDFAAYRS

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.6334

(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	5xcqA	0.61	2.66	0.162	0.705	model1_5xcqA.pdb.gz
2	6cr1H	0.58	3.34	0.132	0.714	model1_6cr1H.pdb.gz
3	3ijhB	0.56	3.53	0.125	0.691	model1_3ijhB.pdb.gz
4	5whzH	0.55	4.22	0.119	0.736	model1_5whzH.pdb.gz
5	1qgc4	0.55	4.21	0.106	0.727	model1_1qgc4.pdb.gz
6	6ul6B	0.54	3.71	0.108	0.686	model1_6ul6B.pdb.gz
7	6xmiB	0.54	3.92	0.101	0.682	model1_6xmiB.pdb.gz
8	3j8dA	0.54	3.52	0.090	0.664	model1_3j8dA.pdb.gz
9	1ce1H	0.54	4.02	0.081	0.696	model1_1ce1H.pdb.gz
10	1mcpH	0.54	3.85	0.121	0.686	model1_1mcpH.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:0004872	0.74	receptor activity
GO:0004871	0.53	signal transducer activity
GO:0038023	0.50	signaling receptor 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:0050863	1.00	regulation of T cell activation
GO:0050670	0.98	regulation of lymphocyte proliferation
GO:0048522	0.95	positive regulation of cellular process
GO:0042129	0.94	regulation of T cell proliferation
GO:0002684	0.94	positive regulation of immune system process
GO:0051239	0.92	regulation of multicellular organismal process
GO:0050870	0.92	positive regulation of T cell activation
GO:0051246	0.89	regulation of protein metabolic process
GO:0031323	0.89	regulation of cellular metabolic process
GO:0010604	0.89	positive regulation of macromolecule metabolic process
GO:0045840	0.88	positive regulation of mitotic nuclear division
GO:0045086	0.88	positive regulation of interleukin-2 biosynthetic process
GO:0042102	0.88	positive regulation of T cell proliferation

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:0044425	0.98	membrane part
GO:0044464	0.97	cell part
GO:0044459	0.86	plasma membrane part
GO:0031224	0.71	intrinsic component of membrane
GO:0016021	0.70	integral component of membrane
GO:0005887	0.68	integral component of plasma membrane
GO:0016020	0.65	membrane
GO:0044424	0.61	intracellular part
GO:0044444	0.57	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	0.066	1zvyA	0.452	1.96	0.152	0.491	3.2.1.17	22,130
2	0.066	1zvhA	0.452	2.13	0.158	0.500	3.2.1.17	22
3	0.060	3bcfA	0.430	4.60	0.044	0.618	3.2.1.98	NA
4	0.060	3fn9C	0.487	4.86	0.087	0.705	3.2.1.23	NA
5	0.060	2d0gA	0.506	4.56	0.059	0.727	3.2.1.135	82

	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	0.02	3phoB	0.546	3.55	0.126	0.682	0.54	KD1	complex1.pdb.gz	89,90,92
2	0.02	1q72H	0.537	4.37	0.130	0.700	0.73	COC	complex2.pdb.gz	56,58,109,110,111,130
3	0.02	1i9jH	0.524	3.73	0.119	0.677	0.83	TES	complex3.pdb.gz	54,67,69,79,115
4	0.02	1kfaH	0.526	4.13	0.112	0.682	0.54	GA4	complex4.pdb.gz	51,52,90,91,94,95
5	0.01	1kcsL	0.449	3.59	0.044	0.577	0.53	III	complex5.pdb.gz	58,109,110,131
6	0.01	2gsiE	0.462	3.65	0.064	0.586	0.70	III	complex6.pdb.gz	58,109,110,132

	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.