D-I-TASSER P29460

D-I-TASSER results for P29460

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

Summary of the Protein

Uniprot ID: P29460
Protein Name: Interleukin-12 subunit beta
Gene Name: IL12B

Input Sequence in FASTA format

>P29460 (328 residues)
MCHQQLVISWFSLVFLASPLVAIWELKKDVYVVELDWYPDAPGEMVVLTCDTPEEDGITW
TLDQSSEVLGSGKTLTIQVKEFGDAGQYTCHKGGEVLSHSLLLLHKKEDGIWSTDILKDQ
KEPKNKTFLRCEAKNYSGRFTCWWLTTISTDLTFSVKSSRGSSDPQGVTCGAATLSAERV
RGDNKEYEYSVECQEDSACPAAEESLPIEVMVDAVHKLKYENYTSSFFIRDIIKPDPPKN
LQLKPLKNSRQVEVSWEYPDTWSTPHSYFSLTFCVQVQGKSKREKKDRVFTDKTSATVIC
RKNASISVRAQDRYYSSSWSEWASVPCS

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	P29460-D1	1-117	117		MCHQQLVISWFSLVFLASPLVAIWELKKDVYVVELDWYPDAPGEMVVLTCDTPEEDGITWTLDQSSEVLGSGKTLTIQVKEFGDAGQYTCHKGGEVLSHSLLLLHKKEDGIWSTDIL
2	P29460-D2	118-231	114		KDQKEPKNKTFLRCEAKNYSGRFTCWWLTTISTDLTFSVKSSRGSSDPQGVTCGAATLSAERVRGDNKEYEYSVECQEDSACPAAEESLPIEVMVDAVHKLKYENYTSSFFIRD
3	P29460-D3	232-328	97		IIKPDPPKNLQLKPLKNSRQVEVSWEYPDTWSTPHSYFSLTFCVQVQGKSKREKKDRVFTDKTSATVICRKNASISVRAQDRYYSSSWSEWASVPCS

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.6

(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	6xayA	0.52	4.39	0.115	0.692	model1_6xayA.pdb.gz
2	6xaxB	0.49	4.76	0.077	0.680	model1_6xaxB.pdb.gz
3	7nwlC	0.49	5.13	0.102	0.701	model1_7nwlC.pdb.gz
4	1e07A	0.49	4.99	0.071	0.695	model1_1e07A.pdb.gz
5	1f42A	0.48	6.13	0.257	0.799	model1_1f42A.pdb.gz
6	5fmvA	0.47	4.90	0.091	0.674	model1_5fmvA.pdb.gz
7	6x3aA	0.47	4.84	0.054	0.643	model1_6x3aA.pdb.gz
8	3l5hA	0.47	3.86	0.071	0.592	model1_3l5hA.pdb.gz
9	3lpwA	0.47	3.51	0.156	0.561	model1_3lpwA.pdb.gz
10	3qt2A	0.47	4.08	0.085	0.598	model1_3qt2A.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:0019955	0.98	cytokine binding
GO:0042164	0.90	interleukin-12 alpha subunit binding
GO:0005102	0.84	receptor binding
GO:0005126	0.80	cytokine receptor binding
GO:0070851	0.79	growth factor receptor binding
GO:0005143	0.76	interleukin-12 receptor binding
GO:0008083	0.68	growth factor activity
GO:0045519	0.66	interleukin-23 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	0.98	biological regulation
GO:0050789	0.98	regulation of biological process
GO:0050794	0.97	regulation of cellular process
GO:0048522	0.95	positive regulation of cellular process
GO:0008284	0.91	positive regulation of cell proliferation
GO:0032946	0.86	positive regulation of mononuclear cell proliferation
GO:0051239	0.80	regulation of multicellular organismal process
GO:0051240	0.79	positive regulation of multicellular organismal process
GO:0080090	0.78	regulation of primary metabolic process
GO:0060255	0.78	regulation of macromolecule metabolic process
GO:0031323	0.78	regulation of cellular metabolic process
GO:0002684	0.78	positive regulation of immune system process
GO:0031325	0.77	positive regulation of cellular metabolic process
GO:0010604	0.77	positive regulation of macromolecule metabolic process
GO:0051247	0.76	positive regulation of protein metabolic process
GO:0050870	0.76	positive regulation of T cell activation
GO:0050671	0.76	positive regulation of lymphocyte proliferation
GO:0001819	0.76	positive regulation of cytokine production
GO:0031326	0.74	regulation of cellular biosynthetic process
GO:0010556	0.74	regulation of macromolecule biosynthetic process
GO:0031328	0.73	positive regulation of cellular biosynthetic process
GO:0010557	0.73	positive regulation of macromolecule biosynthetic process
GO:0046635	0.71	positive regulation of alpha-beta T cell activation
GO:0045078	0.71	positive regulation of interferon-gamma biosynthetic process
GO:0051135	0.70	positive regulation of NK T cell activation
GO:0032816	0.70	positive regulation of natural killer cell activation
GO:0002376	0.62	immune system process
GO:0044699	0.61	single-organism process
GO:0009987	0.59	cellular process
GO:0050896	0.58	response to stimulus
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:0044421	0.99	extracellular region part
GO:0043234	0.98	protein complex
GO:0043514	0.93	interleukin-12 complex
GO:0044464	0.69	cell part
GO:0070743	0.68	interleukin-23 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

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	7reqD	0.370	7.17	0.049	0.689	5.4.99.2	35,69,75
2	0.060	2vdcA	0.374	6.79	0.032	0.655	1.4.1.13	NA
3	0.060	2q3zA	0.401	6.52	0.063	0.665	2.3.2.13	NA
4	0.060	1wd9A	0.399	6.86	0.064	0.701	3.5.3.15	NA
5	0.060	2ow6A	0.365	7.01	0.082	0.643	3.2.1.114	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	1mq80	0.310	4.72	0.099	0.424	0.63	III	complex1.pdb.gz	60,61,87,89,91,93,95
	2	0.01	3mzgB	0.410	4.36	0.075	0.552	0.58	NA	complex2.pdb.gz	57,58,59,91

	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.