D-I-TASSER P04085

D-I-TASSER results for P04085

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

Summary of the Protein

Uniprot ID: P04085
Protein Name: Platelet-derived growth factor subunit A
Gene Name: PDGFA

Input Sequence in FASTA format

>P04085 (211 residues)
MRTLACLLLLGCGYLAHVLAEEAEIPREVIERLARSQIHSIRDLQRLLEIDSVGSEDSLD
TSLRAHGVHATKHVPEKRPLPIRRKRSIEEAVPAVCKTRTVIYEIPRSQVDPTSANFLIW
PPCVEVKRCTGCCNTSSVKCQPSRVHHRSVKVAKVEYVRKKPKLKEVQVRLEEHLECACA
TTSLNPDYREEDTGRPRESGKKRKRKRLKPT

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	P04085-D1	1-211	211		MRTLACLLLLGCGYLAHVLAEEAEIPREVIERLARSQIHSIRDLQRLLEIDSVGSEDSLDTSLRAHGVHATKHVPEKRPLPIRRKRSIEEAVPAVCKTRTVIYEIPRSQVDPTSANFLIWPPCVEVKRCTGCCNTSSVKCQPSRVHHRSVKVAKVEYVRKKPKLKEVQVRLEEHLECACATTSLNPDYREEDTGRPRESGKKRKRKRLKPT

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.5574

(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	3mjkA	0.56	2.01	0.915	0.607	model1_3mjkA.pdb.gz
2	4zgvA	0.43	6.17	0.055	0.801	model1_4zgvA.pdb.gz
3	1kekA	0.42	5.39	0.038	0.697	model1_1kekA.pdb.gz
4	6l7iF1	0.42	6.18	0.032	0.782	model1_6l7iF1.pdb.gz
5	5fr8A	0.42	5.79	0.045	0.749	model1_5fr8A.pdb.gz
6	5mzsA	0.42	6.12	0.031	0.754	model1_5mzsA.pdb.gz
7	5fj8O	0.42	5.62	0.050	0.720	model1_5fj8O.pdb.gz
8	1xkwA	0.42	5.50	0.026	0.720	model1_1xkwA.pdb.gz
9	2hdiA	0.39	5.97	0.036	0.716	model1_2hdiA.pdb.gz
10	1fepA	0.39	5.98	0.038	0.701	model1_1fepA.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	0.99	receptor binding
GO:0070851	0.98	growth factor receptor binding
GO:0005161	0.88	platelet-derived growth factor 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:0065007	0.94	biological regulation
GO:0050794	0.93	regulation of cellular process
GO:0044699	0.93	single-organism process
GO:0048518	0.87	positive regulation of biological process
GO:0080090	0.86	regulation of primary metabolic process
GO:0060255	0.86	regulation of macromolecule metabolic process
GO:0048522	0.86	positive regulation of cellular process
GO:0031323	0.86	regulation of cellular metabolic process
GO:0008284	0.83	positive regulation of cell proliferation
GO:0048583	0.82	regulation of response to stimulus
GO:0031325	0.82	positive regulation of cellular metabolic process
GO:0010604	0.82	positive regulation of macromolecule metabolic process
GO:0001932	0.82	regulation of protein phosphorylation
GO:0007165	0.81	signal transduction
GO:0001934	0.81	positive regulation of protein phosphorylation
GO:0007166	0.80	cell surface receptor signaling pathway
GO:0007169	0.79	transmembrane receptor protein tyrosine kinase signaling pathway
GO:0032501	0.78	multicellular organismal process
GO:0048584	0.77	positive regulation of response to stimulus
GO:0032879	0.77	regulation of localization
GO:0031954	0.77	positive regulation of protein autophosphorylation
GO:0009966	0.77	regulation of signal transduction
GO:0030335	0.76	positive regulation of cell migration
GO:1902531	0.75	regulation of intracellular signal transduction
GO:0065008	0.75	regulation of biological quality
GO:0070374	0.74	positive regulation of ERK1 and ERK2 cascade
GO:0043085	0.74	positive regulation of catalytic activity
GO:0050878	0.73	regulation of body fluid levels
GO:0048008	0.73	platelet-derived growth factor receptor signaling pathway
GO:0044707	0.73	single-multicellular organism process
GO:0043406	0.73	positive regulation of MAP kinase activity
GO:0014068	0.73	positive regulation of phosphatidylinositol 3-kinase signaling
GO:0007596	0.64	blood coagulation

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	0.96	extracellular region part
GO:0005615	0.95	extracellular space
GO:0044464	0.75	cell part
GO:0044424	0.59	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	0.060	1b0pA	0.423	5.31	0.029	0.692	1.2.7.1	NA
2	0.060	1kblA	0.405	6.05	0.043	0.749	2.7.9.1	NA
3	0.060	1e7pA	0.377	5.84	0.059	0.673	1.3.99.1	NA
4	0.060	1kc7A	0.405	6.15	0.026	0.758	2.7.9.1	NA
5	0.060	3eqlM	0.355	6.05	0.044	0.649	2.7.7.6	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:

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	1b0pA	0.423	5.31	0.029	0.692	0.37	SF4	complex1.pdb.gz	140,141,176,177,178,179
2	0.01	2iahA	0.405	5.86	0.042	0.706	0.31	PVE	complex2.pdb.gz	133,137,142
3	0.01	2c3oB	0.424	5.39	0.029	0.697	0.20	SF4	complex3.pdb.gz	177,178,179,180,181
4	0.01	2w78B	0.407	5.76	0.057	0.706	0.26	PVE	complex4.pdb.gz	131,133,136
5	0.01	2c3uA	0.423	5.27	0.033	0.687	0.22	SF4	complex5.pdb.gz	95,96,131

	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.