D-I-TASSER P02776

D-I-TASSER results for P02776

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

Summary of the Protein

Uniprot ID: P02776
Protein Name: Platelet factor 4
Gene Name: PF4

Input Sequence in FASTA format

>P02776 (101 residues)
MSSAAGFCASRPGLLFLGLLLLPLVVAFASAEAEEDGDLQCLCVKTTSQVRPRHITSLEV
IKAGPHCPTAQLIATLKNGRKICLDLQAPLYKKIIKKLLES

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	P02776-D1	1-101	101		MSSAAGFCASRPGLLFLGLLLLPLVVAFASAEAEEDGDLQCLCVKTTSQVRPRHITSLEVIKAGPHCPTAQLIATLKNGRKICLDLQAPLYKKIIKKLLES

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.6333

(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	1f9pA	0.64	2.48	0.474	0.772	model1_1f9pA.pdb.gz
2	1mgsA	0.59	2.09	0.449	0.673	model1_1mgsA.pdb.gz
3	1o80A	0.58	1.47	0.304	0.644	model1_1o80A.pdb.gz
4	2mgsA	0.58	1.42	0.424	0.644	model1_2mgsA.pdb.gz
5	1ilqA	0.57	1.55	0.364	0.644	model1_1ilqA.pdb.gz
6	1eotA	0.56	1.78	0.239	0.663	model1_1eotA.pdb.gz
7	2l4nA	0.54	2.19	0.134	0.663	model1_2l4nA.pdb.gz
8	4zaiA	0.54	2.11	0.254	0.634	model1_4zaiA.pdb.gz
9	1g91A	0.53	2.08	0.162	0.653	model1_1g91A.pdb.gz
10	3fpuB	0.53	1.97	0.185	0.624	model1_3fpuB.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:0045236	0.98	CXCR chemokine receptor binding
GO:0008009	0.93	chemokine 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:0050794	1.00	regulation of cellular process
GO:0048518	1.00	positive regulation of biological process
GO:0002376	0.98	immune system process
GO:0048522	0.94	positive regulation of cellular process
GO:0050896	0.93	response to stimulus
GO:0040017	0.93	positive regulation of locomotion
GO:0048584	0.92	positive regulation of response to stimulus
GO:0032879	0.92	regulation of localization
GO:0002682	0.92	regulation of immune system process
GO:0042127	0.91	regulation of cell proliferation
GO:0002687	0.91	positive regulation of leukocyte migration
GO:0042221	0.89	response to chemical
GO:0032103	0.89	positive regulation of response to external stimulus
GO:0006950	0.89	response to stress
GO:1901700	0.88	response to oxygen-containing compound
GO:0050921	0.88	positive regulation of chemotaxis
GO:0010033	0.88	response to organic substance
GO:0007165	0.88	signal transduction
GO:0019221	0.86	cytokine-mediated signaling pathway
GO:0007186	0.86	G-protein coupled receptor signaling pathway
GO:0002690	0.86	positive regulation of leukocyte chemotaxis
GO:0070098	0.85	chemokine-mediated signaling pathway
GO:0033993	0.85	response to lipid
GO:0006955	0.85	immune response
GO:0006952	0.85	defense response
GO:0002237	0.85	response to molecule of bacterial origin
GO:0032496	0.84	response to lipopolysaccharide
GO:0006954	0.84	inflammatory response
GO:0044699	0.57	single-organism process
GO:0009987	0.57	cellular process
GO:0044763	0.51	single-organism cellular 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:0005615	0.99	extracellular space
GO:0044464	0.52	cell 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	1eusA	0.434	4.37	0.011	0.782	3.2.1.18	NA
2	0.060	1sliA	0.440	4.26	0.054	0.762	4.2.2.15 3.2.1.18	NA
3	0.060	1j36A	0.454	4.67	0.040	0.832	3.4.15.1	NA
4	0.060	1af2A	0.455	3.72	0.037	0.752	3.5.4.5	NA
5	0.060	2z8kD	0.359	4.18	0.081	0.653	2.3.2.2	57

	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	0.06	1icw0	0.571	1.42	0.359	0.634	1.26	III	complex1.pdb.gz	56,57,58,59,60,62,63,70,87,92,95,98,99
2	0.03	1cm90	0.498	1.90	0.188	0.584	0.91	III	complex2.pdb.gz	43,45,46,64,67,68,73,81,82,83
3	0.03	1dok0	0.541	1.84	0.157	0.624	0.79	III	complex3.pdb.gz	43,44,45,46,54,65,73,76,78,80,81,82,83
4	0.03	1nr40	0.524	1.90	0.167	0.624	0.75	III	complex4.pdb.gz	56,59,75,79,81,83
5	0.03	1b3aB	0.527	2.16	0.121	0.624	1.18	SO4	complex5.pdb.gz	54,76,77,78,80
6	0.02	1eqt0	0.525	1.88	0.136	0.614	0.89	III	complex6.pdb.gz	42,43,44,46,73,83

	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, Qiqige Wuyun, Yang Li, Quancheng Liu, Xiaogen Zhou, Yiheng Zhu, P. Lydia Freddolino, Yang Zhang. Integrating deep learning potentials with I-TASSER for single- and multi-domain protein structure prediction. Submitted. 2023.