D-I-TASSER Q53EL6

D-I-TASSER results for Q53EL6

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

Summary of the Protein

Uniprot ID: Q53EL6
Protein Name: Programmed cell death protein 4
Gene Name: PDCD4

Input Sequence in FASTA format

>Q53EL6 (469 residues)
MDVENEQILNVNPADPDNLSDSLFSGDEENAGTEEIKNEINGNWISASSINEARINAKAK
RRLRKNSSRDSGRGDSVSDSGSDALRSGLTVPTSPKGRLLDRRSRSGKGRGLPKKGGAGG
KGVWGTPGQVYDVEEVDVKDPNYDDDQENCVYETVVLPLDERAFEKTLTPIIQEYFEHGD
TNEVAEMLRDLNLGEMKSGVPVLAVSLALEGKASHREMTSKLLSDLCGTVMSTTDVEKSF
DKLLKDLPELALDTPRAPQLVGQFIARAVGDGILCNTYIDSYKGTVDCVQARAALDKATV
LLSMSKGGKRKDSVWGSGGGQQSVNHLVKEIDMLLKEYLLSGDISEAEHCLKELEVPHFH
HELVYEAIIMVLESTGESTFKMILDLLKSLWKSSTITVDQMKRGYERIYNEIPDINLDVP
HSYSVLERFVEECFQAGIISKQLRDLCPSRGRKRFVSEGDGGRLKPESY

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	Q53EL6-D1	1-469	469		MDVENEQILNVNPADPDNLSDSLFSGDEENAGTEEIKNEINGNWISASSINEARINAKAKRRLRKNSSRDSGRGDSVSDSGSDALRSGLTVPTSPKGRLLDRRSRSGKGRGLPKKGGAGGKGVWGTPGQVYDVEEVDVKDPNYDDDQENCVYETVVLPLDERAFEKTLTPIIQEYFEHGDTNEVAEMLRDLNLGEMKSGVPVLAVSLALEGKASHREMTSKLLSDLCGTVMSTTDVEKSFDKLLKDLPELALDTPRAPQLVGQFIARAVGDGILCNTYIDSYKGTVDCVQARAALDKATVLLSMSKGGKRKDSVWGSGGGQQSVNHLVKEIDMLLKEYLLSGDISEAEHCLKELEVPHFHHELVYEAIIMVLESTGESTFKMILDLLKSLWKSSTITVDQMKRGYERIYNEIPDINLDVPHSYSVLERFVEECFQAGIISKQLRDLCPSRGRKRFVSEGDGGRLKPESY

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.6535

(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	6n1zA	0.54	6.53	0.065	0.823	model1_6n1zA.pdb.gz
2	5dlqB	0.53	6.39	0.075	0.793	model1_5dlqB.pdb.gz
3	6fvbA	0.53	6.92	0.064	0.829	model1_6fvbA.pdb.gz
4	3a6pA	0.52	6.70	0.056	0.815	model1_3a6pA.pdb.gz
5	6xjpC	0.52	6.94	0.070	0.819	model1_6xjpC.pdb.gz
6	4fgvA	0.52	6.84	0.057	0.808	model1_4fgvA.pdb.gz
7	4ifqA	0.51	6.83	0.048	0.797	model1_4ifqA.pdb.gz
8	4c0oA	0.51	7.06	0.079	0.819	model1_4c0oA.pdb.gz
9	6tnfB	0.50	6.44	0.053	0.750	model1_6tnfB.pdb.gz
10	6jxaA	0.50	6.62	0.073	0.761	model1_6jxaA.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:1901363	0.62	heterocyclic compound binding
GO:0097159	0.62	organic cyclic compound binding
GO:0008190	0.57	eukaryotic initiation factor 4E binding
GO:0003676	0.55	nucleic acid 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:0044699	0.90	single-organism process
GO:0044767	0.84	single-organism developmental process
GO:0065007	0.80	biological regulation
GO:0050789	0.79	regulation of biological process
GO:0050794	0.78	regulation of cellular process
GO:0009987	0.74	cellular process
GO:0080090	0.68	regulation of primary metabolic process
GO:0031323	0.68	regulation of cellular metabolic process
GO:0060255	0.67	regulation of macromolecule metabolic process
GO:2000112	0.64	regulation of cellular macromolecule biosynthetic process
GO:0051171	0.64	regulation of nitrogen compound metabolic process
GO:0032268	0.64	regulation of cellular protein metabolic process
GO:0010468	0.64	regulation of gene expression
GO:0048519	0.58	negative regulation of biological process
GO:0044763	0.58	single-organism cellular process
GO:0048523	0.57	negative regulation of cellular process
GO:0006355	0.55	regulation of transcription, DNA-templated
GO:0048583	0.54	regulation of response to stimulus
GO:0032269	0.54	negative regulation of cellular protein metabolic process
GO:0031399	0.54	regulation of protein modification process
GO:0023051	0.54	regulation of signaling
GO:0010646	0.54	regulation of cell communication
GO:2000113	0.53	negative regulation of cellular macromolecule biosynthetic process
GO:1902531	0.53	regulation of intracellular signal transduction
GO:0051172	0.53	negative regulation of nitrogen compound metabolic process
GO:0050790	0.53	regulation of catalytic activity
GO:0048869	0.53	cellular developmental process
GO:0010629	0.53	negative regulation of gene expression
GO:0001932	0.53	regulation of protein phosphorylation
GO:0045892	0.52	negative regulation of transcription, DNA-templated
GO:0043508	0.52	negative regulation of JUN kinase activity
GO:0007569	0.52	cell aging

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:0005737	0.85	cytoplasm
GO:0044444	0.71	cytoplasmic part
GO:0005829	0.63	cytosol
GO:0043226	0.61	organelle
GO:0043229	0.60	intracellular organelle
GO:0043227	0.59	membrane-bounded organelle
GO:0043231	0.58	intracellular membrane-bounded organelle
GO:0005634	0.54	nucleus

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	2x0sA	0.369	7.18	0.035	0.608	2.7.9.1	NA
2	0.060	1ea0A	0.374	7.66	0.032	0.655	1.4.1.13	NA
3	0.060	3c5wA	0.260	4.97	0.088	0.341	3.1.3.16	NA
4	0.060	2pffB	0.307	7.28	0.046	0.512	2.3.1.86	NA
5	0.060	2np0A	0.370	7.24	0.046	0.616	3.4.24.69	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:

Click to view	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	2ot8A	0.431	7.38	0.060	0.727	0.20	III	complex1.pdb.gz	194,227,228
	2	0.01	3lwwC	0.453	6.91	0.067	0.719	0.10	III	complex2.pdb.gz	176,225,228

	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.