D-I-TASSER P46527

D-I-TASSER results for P46527

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

Summary of the Protein

Uniprot ID: P46527
Protein Name: Cyclin-dependent kinase inhibitor 1B
Gene Name: CDKN1B

Input Sequence in FASTA format

>P46527 (198 residues)
MSNVRVSNGSPSLERMDARQAEHPKPSACRNLFGPVDHEELTRDLEKHCRDMEEASQRKW
NFDFQNHKPLEGKYEWQEVEKGSLPEFYYRPPRPPKGACKVPAQESQDVSGSRPAAPLIG
APANSEDTHLVDPKTDPSDSQTGLAEQCAGIRKRPATDDSSTQNKRANRTEENVSDGSPN
AGSVEQTPKKPGLRRRQT

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	P46527-D1	1-198	198		MSNVRVSNGSPSLERMDARQAEHPKPSACRNLFGPVDHEELTRDLEKHCRDMEEASQRKWNFDFQNHKPLEGKYEWQEVEKGSLPEFYYRPPRPPKGACKVPAQESQDVSGSRPAAPLIGAPANSEDTHLVDPKTDPSDSQTGLAEQCAGIRKRPATDDSSTQNKRANRTEENVSDGSPNAGSVEQTPKKPGLRRRQT

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.4431

(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	2g3fA	0.48	5.46	0.053	0.833	model1_2g3fA.pdb.gz
2	3e0lA	0.47	5.51	0.038	0.803	model1_3e0lA.pdb.gz
3	6oh9A	0.47	5.46	0.054	0.823	model1_6oh9A.pdb.gz
4	4f0lA	0.47	5.68	0.105	0.833	model1_4f0lA.pdb.gz
5	2oofA	0.47	5.94	0.047	0.849	model1_2oofA.pdb.gz
6	4v1xA	0.47	5.63	0.048	0.823	model1_4v1xA.pdb.gz
7	2qt3A	0.47	5.68	0.033	0.808	model1_2qt3A.pdb.gz
8	6sj0A	0.47	5.91	0.068	0.849	model1_6sj0A.pdb.gz
9	6ohbA	0.47	5.32	0.060	0.793	model1_6ohbA.pdb.gz
10	2oodA	0.47	5.74	0.065	0.813	model1_2oodA.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:0098772	0.48	molecular function regulator
GO:0030234	0.47	enzyme regulator activity
GO:0019887	0.46	protein kinase regulator activity
GO:0004857	0.46	enzyme inhibitor activity
GO:0004861	0.45	cyclin-dependent protein serine/threonine kinase inhibitor activity
GO:0019899	0.41	enzyme binding
GO:0008047	0.38	enzyme activator activity
GO:0061134	0.33	peptidase regulator activity
GO:0019902	0.33	phosphatase binding
GO:0019903	0.32	protein phosphatase binding
GO:0008656	0.32	cysteine-type endopeptidase activator activity involved in apoptotic 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 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	0.97	biological regulation
GO:0050794	0.95	regulation of cellular process
GO:0044699	0.94	single-organism process
GO:0009987	0.93	cellular process
GO:0048523	0.89	negative regulation of cellular process
GO:0031323	0.87	regulation of cellular metabolic process
GO:0080090	0.84	regulation of primary metabolic process
GO:0060255	0.84	regulation of macromolecule metabolic process
GO:0044763	0.83	single-organism cellular process
GO:0051726	0.81	regulation of cell cycle
GO:0048518	0.78	positive regulation of biological process
GO:0048522	0.77	positive regulation of cellular process
GO:0045786	0.77	negative regulation of cell cycle
GO:0050896	0.76	response to stimulus
GO:0031325	0.72	positive regulation of cellular metabolic process
GO:0042325	0.70	regulation of phosphorylation
GO:0031324	0.70	negative regulation of cellular metabolic process
GO:0042326	0.69	negative regulation of phosphorylation
GO:0065009	0.68	regulation of molecular function
GO:0051338	0.67	regulation of transferase activity
GO:0010605	0.67	negative regulation of macromolecule metabolic process
GO:0043549	0.66	regulation of kinase activity
GO:0008285	0.66	negative regulation of cell proliferation
GO:0044092	0.64	negative regulation of molecular function
GO:0032268	0.64	regulation of cellular protein metabolic process
GO:0033673	0.63	negative regulation of kinase activity
GO:0031399	0.63	regulation of protein modification process
GO:0010604	0.63	positive regulation of macromolecule metabolic process
GO:0051171	0.62	regulation of nitrogen compound metabolic process
GO:0031326	0.62	regulation of cellular biosynthetic process
GO:0010556	0.62	regulation of macromolecule biosynthetic process
GO:0001932	0.62	regulation of protein phosphorylation
GO:2000112	0.61	regulation of cellular macromolecule biosynthetic process
GO:0019219	0.61	regulation of nucleobase-containing compound metabolic process
GO:0000079	0.61	regulation of cyclin-dependent protein serine/threonine kinase activity
GO:0042221	0.60	response to chemical
GO:0032270	0.57	positive regulation of cellular protein metabolic process
GO:0043085	0.56	positive regulation of catalytic activity
GO:0032502	0.55	developmental process
GO:0010038	0.55	response to metal ion
GO:0008219	0.55	cell death
GO:0022402	0.54	cell cycle process
GO:0007050	0.53	cell cycle arrest
GO:0006950	0.53	response to stress
GO:0051716	0.50	cellular response to stimulus
GO:0010468	0.50	regulation of gene expression

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	1.00	intracellular part
GO:0043231	0.98	intracellular membrane-bounded organelle
GO:0005634	0.97	nucleus
GO:0005737	0.74	cytoplasm
GO:0044444	0.63	cytoplasmic part
GO:0032991	0.62	macromolecular complex
GO:0043234	0.60	protein complex
GO:0005829	0.54	cytosol

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	2osxA	0.444	5.23	0.039	0.748	3.2.1.123	NA
2	0.060	1dwaM	0.438	5.87	0.067	0.803	3.2.1.147	NA
3	0.060	2zoxA	0.443	5.74	0.058	0.778	3.2.1.21	NA
4	0.060	2qubA	0.412	5.82	0.068	0.727	3.1.1.3	NA
5	0.060	1qoxM	0.426	5.70	0.045	0.758	3.2.1.21	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:

No Binding sites was predicted

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

	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.