D-I-TASSER P24385

D-I-TASSER results for P24385

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

Summary of the Protein

Uniprot ID: P24385
Protein Name: G1/S-specific cyclin-D1
Gene Name: CCND1

Input Sequence in FASTA format

>P24385 (295 residues)
MEHQLLCCEVETIRRAYPDANLLNDRVLRAMLKAEETCAPSVSYFKCVQKEVLPSMRKIV
ATWMLEVCEEQKCEEEVFPLAMNYLDRFLSLEPVKKSRLQLLGATCMFVASKMKETIPLT
AEKLCIYTDNSIRPEELLQMELLLVNKLKWNLAAMTPHDFIEHFLSKMPEAEENKQIIRK
HAQTFVALCATDVKFISNPPSMVAAGSVVAAVQGLNLRSPNNFLSYYRLTRFLSRVIKCD
PDCLRACQEQIEALLESSLRQAQQNMDPKAAEEEEEEEEEVDLACTPTDVRDVDI

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	P24385-D1	1-295	295		MEHQLLCCEVETIRRAYPDANLLNDRVLRAMLKAEETCAPSVSYFKCVQKEVLPSMRKIVATWMLEVCEEQKCEEEVFPLAMNYLDRFLSLEPVKKSRLQLLGATCMFVASKMKETIPLTAEKLCIYTDNSIRPEELLQMELLLVNKLKWNLAAMTPHDFIEHFLSKMPEAEENKQIIRKHAQTFVALCATDVKFISNPPSMVAAGSVVAAVQGLNLRSPNNFLSYYRLTRFLSRVIKCDPDCLRACQEQIEALLESSLRQAQQNMDPKAAEEEEEEEEEVDLACTPTDVRDVDI

Top 1 final models from D-I-TASSER

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Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.8478

(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

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Top 10 structural analogs in PDB (as identified by TM-align)

Rank	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	Download Alignment
1	2w96A	0.83	1.01	0.992	0.844	model1_2w96A.pdb.gz
2	3ddpD	0.81	2.07	0.238	0.881	model1_3ddpD.pdb.gz
3	6gu2B	0.79	2.55	0.208	0.878	model1_6gu2B.pdb.gz
4	2eufA	0.74	2.27	0.234	0.810	model1_2eufA.pdb.gz
5	1w98B	0.71	3.31	0.229	0.824	model1_1w98B.pdb.gz
6	2w2hA	0.65	3.46	0.127	0.786	model1_2w2hA.pdb.gz
7	2i53A	0.62	3.28	0.159	0.739	model1_2i53A.pdb.gz
8	3g33D1	0.44	0.88	0.598	0.448	model1_3g33D1.pdb.gz
9	1g3nC1	0.43	1.20	0.356	0.448	model1_1g3nC1.pdb.gz
10	1f5qD1	0.35	2.02	0.245	0.373	model1_1f5qD1.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:0030234	0.31	enzyme regulator activity
GO:0000988	0.30	transcription factor activity, protein 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	0.93	biological regulation
GO:0050789	0.92	regulation of biological process
GO:0050794	0.91	regulation of cellular process
GO:0009987	0.89	cellular process
GO:0051726	0.78	regulation of cell cycle
GO:0048518	0.78	positive regulation of biological process
GO:0048522	0.77	positive regulation of cellular process
GO:0080090	0.73	regulation of primary metabolic process
GO:0060255	0.73	regulation of macromolecule metabolic process
GO:0031323	0.73	regulation of cellular metabolic process
GO:0032268	0.65	regulation of cellular protein metabolic process
GO:0065009	0.64	regulation of molecular function
GO:0031399	0.64	regulation of protein modification process
GO:0022402	0.64	cell cycle process
GO:0045787	0.63	positive regulation of cell cycle
GO:0031325	0.63	positive regulation of cellular metabolic process
GO:0010604	0.63	positive regulation of macromolecule metabolic process
GO:0001932	0.63	regulation of protein phosphorylation
GO:0051338	0.62	regulation of transferase activity
GO:0050896	0.61	response to stimulus
GO:0045859	0.61	regulation of protein kinase activity
GO:1903047	0.60	mitotic cell cycle process
GO:0000079	0.60	regulation of cyclin-dependent protein serine/threonine kinase activity
GO:0048519	0.58	negative regulation of biological process
GO:0031401	0.58	positive regulation of protein modification process
GO:0010564	0.58	regulation of cell cycle process
GO:0048523	0.57	negative regulation of cellular process
GO:0001934	0.57	positive regulation of protein phosphorylation
GO:0051347	0.56	positive regulation of transferase activity
GO:0044772	0.56	mitotic cell cycle phase transition
GO:0051716	0.55	cellular response to stimulus
GO:0045737	0.55	positive regulation of cyclin-dependent protein serine/threonine kinase activity
GO:0007346	0.54	regulation of mitotic cell cycle
GO:0045786	0.53	negative regulation of cell cycle
GO:0000082	0.53	G1/S transition of mitotic cell cycle
GO:0010948	0.52	negative regulation of cell cycle process
GO:0006950	0.52	response to stress
GO:1901987	0.51	regulation of cell cycle phase transition
GO:0033554	0.51	cellular response to stress
GO:1901990	0.50	regulation of mitotic cell cycle phase transition

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:0044424	0.99	intracellular part
GO:0043229	0.87	intracellular organelle
GO:0043227	0.84	membrane-bounded organelle
GO:0043231	0.83	intracellular membrane-bounded organelle
GO:0005634	0.82	nucleus
GO:0032991	0.78	macromolecular complex
GO:0043234	0.76	protein complex
GO:1990234	0.68	transferase complex
GO:1902554	0.65	serine/threonine protein kinase complex
GO:0000307	0.64	cyclin-dependent protein kinase holoenzyme complex

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

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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	1lrwC	0.403	6.56	0.045	0.705	1.1.99.8	NA
2	0.060	1oj7A	0.402	5.49	0.045	0.610	1.1.1.-	NA
3	0.060	3dsiA	0.402	6.61	0.073	0.709	4.2.1.92	NA
4	0.060	1q50A	0.392	6.24	0.078	0.664	5.3.1.9	NA
5	0.060	1vncA	0.455	6.05	0.033	0.742	1.11.1.10	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

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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	0.05	1g3n1	0.736	1.92	0.288	0.790	0.34	III	complex1.pdb.gz	31,34,38,112,113,120,121,141,151,152,154
2	0.03	1f5q1	0.703	3.01	0.176	0.807	0.19	III	complex2.pdb.gz	17,108,120
3	0.01	2ong0	0.432	5.93	0.047	0.688	0.19	III	complex3.pdb.gz	270,274,275
4	0.01	2ongA	0.432	5.93	0.047	0.688	0.14	FPG	complex4.pdb.gz	31,35,160

	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.