D-I-TASSER P29350

D-I-TASSER results for P29350

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

Summary of the Protein

Uniprot ID: P29350
Protein Name: Tyrosine-protein phosphatase non-receptor type 6
Gene Name: PTPN6

Input Sequence in FASTA format

>P29350 (595 residues)
MVRWFHRDLSGLDAETLLKGRGVHGSFLARPSRKNQGDFSLSVRVGDQVTHIRIQNSGDF
YDLYGGEKFATLTELVEYYTQQQGVLQDRDGTIIHLKYPLNCSDPTSERWYHGHMSGGQA
ETLLQAKGEPWTFLVRESLSQPGDFVLSVLSDQPKAGPGSPLRVTHIKVMCEGGRYTVGG
LETFDSLTDLVEHFKKTGIEEASGAFVYLRQPYYATRVNAADIENRVLELNKKQESEDTA
KAGFWEEFESLQKQEVKNLHQRLEGQRPENKGKNRYKNILPFDHSRVILQGRDSNIPGSD
YINANYIKNQLLGPDENAKTYIASQGCLEATVNDFWQMAWQENSRVIVMTTREVEKGRNK
CVPYWPEVGMQRAYGPYSVTNCGEHDTTEYKLRTLQVSPLDNGDLIREIWHYQYLSWPDH
GVPSEPGGVLSFLDQINQRQESLPHAGPIIVHCSAGIGRTGTIIVIDMLMENISTKGLDC
DIDIQKTIQMVRAQRSGMVQTEAQYKFIYVAIAQFIETTKKKLEVLQSQKGQESEYGNIT
YPPAMKNAHAKASRTSSKHKEDVYENLHTKNKREEKVKKQRSADKEKSKGSLKRK

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	P29350-D1	1-106	106		MVRWFHRDLSGLDAETLLKGRGVHGSFLARPSRKNQGDFSLSVRVGDQVTHIRIQNSGDFYDLYGGEKFATLTELVEYYTQQQGVLQDRDGTIIHLKYPLNCSDPT
2	P29350-D2	107-167	61		SERWYHGHMSGGQAETLLQAKGEPWTFLVRESLSQPGDFVLSVLSDQPKAGPGSPLRVTHI
3	P29350-D3	168-213	46		KVMCEGGRYTVGGLETFDSLTDLVEHFKKTGIEEASGAFVYLRQPY
4	P29350-D4	214-595	382		YATRVNAADIENRVLELNKKQESEDTAKAGFWEEFESLQKQEVKNLHQRLEGQRPENKGKNRYKNILPFDHSRVILQGRDSNIPGSDYINANYIKNQLLGPDENAKTYIASQGCLEATVNDFWQMAWQENSRVIVMTTREVEKGRNKCVPYWPEVGMQRAYGPYSVTNCGEHDTTEYKLRTLQVSPLDNGDLIREIWHYQYLSWPDHGVPSEPGGVLSFLDQINQRQESLPHAGPIIVHCSAGIGRTGTIIVIDMLMENISTKGLDCDIDIQKTIQMVRAQRSGMVQTEAQYKFIYVAIAQFIETTKKKLEVLQSQKGQESEYGNITYPPAMKNAHAKASRTSSKHKEDVYENLHTKNKREEKVKKQRSADKEKSKGSLKRK

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.76

(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	2shpA	0.68	4.35	0.551	0.812	model1_2shpA.pdb.gz
2	2b3oA	0.61	4.43	0.593	0.718	model1_2b3oA.pdb.gz
3	1larA	0.51	3.97	0.322	0.573	model1_1larA.pdb.gz
4	1yguB	0.51	3.93	0.299	0.573	model1_1yguB.pdb.gz
5	2nlkA	0.51	3.48	0.325	0.556	model1_2nlkA.pdb.gz
6	2jjdF	0.50	3.32	0.329	0.546	model1_2jjdF.pdb.gz
7	2f6fA	0.47	2.43	0.314	0.499	model1_2f6fA.pdb.gz
8	2pi7A	0.47	1.89	0.377	0.491	model1_2pi7A.pdb.gz
9	2hc1A	0.47	1.99	0.355	0.486	model1_2hc1A.pdb.gz
10	3s3eA	0.47	1.81	0.348	0.482	model1_3s3eA.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:0003824	0.85	catalytic activity
GO:0042578	0.61	phosphoric ester hydrolase activity
GO:0016791	0.59	phosphatase activity
GO:0004721	0.55	phosphoprotein phosphatase activity
GO:0004725	0.52	protein tyrosine phosphatase 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:0065007	0.88	biological regulation
GO:0050789	0.87	regulation of biological process
GO:0050794	0.85	regulation of cellular process
GO:0044699	0.81	single-organism process
GO:0009987	0.79	cellular process
GO:0071704	0.64	organic substance metabolic process
GO:0044763	0.64	single-organism cellular process
GO:0044237	0.64	cellular metabolic process
GO:0044238	0.63	primary metabolic process
GO:0006796	0.61	phosphate-containing compound metabolic process
GO:0044260	0.60	cellular macromolecule metabolic process
GO:0019538	0.59	protein metabolic process
GO:0006464	0.58	cellular protein modification process
GO:0007165	0.57	signal transduction

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	0.87	intracellular part
GO:0044425	0.53	membrane part
GO:0016020	0.52	membrane
GO:0044444	0.51	cytoplasmic part
GO:0043226	0.51	organelle
GO:0043227	0.50	membrane-bounded organelle

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	0.260	2qdpA	0.451	2.89	0.336	0.487	3.1.3.48	286,302,306,342,447
2	0.228	2nz6A	0.451	2.49	0.318	0.477	3.1.3.48	459
3	0.105	2nv5A	0.463	1.52	0.382	0.476	3.1.3.48	327
4	0.102	2ooqB	0.460	1.57	0.427	0.472	3.1.3.48	NA
5	0.100	2hc1A	0.463	1.99	0.358	0.482	3.1.3.48	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	0.87	1fprA	0.455	1.99	0.936	0.474	1.57	III	complex1.pdb.gz	275,276,278,279,282,453,454,455,457,459,492,496,497,500
2	0.40	2h04A	0.455	1.69	0.364	0.471	1.19	4UN	complex2.pdb.gz	276,277,278,453,454,455,456,457,458,459,497
3	0.38	1nwlA	0.455	1.79	0.339	0.471	1.25	964	complex3.pdb.gz	275,276,277,455,457,458,459,500,504
4	0.34	3eaxA	0.454	1.77	0.337	0.469	0.90	LZP	complex4.pdb.gz	454,455,458,459,500
5	0.32	1kakA	0.468	2.40	0.323	0.494	0.80	FNP	complex5.pdb.gz	276,454,455,457,459,498
6	0.05	2b4s1	0.455	2.39	0.315	0.481	1.08	III	complex6.pdb.gz	231,232,352,360,386,387,388,389,418,422,423,425,431,503,506

	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.