D-I-TASSER P42701

D-I-TASSER results for P42701

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

Summary of the Protein

Uniprot ID: P42701
Protein Name: Interleukin-12 receptor subunit beta-1
Gene Name: IL12RB1

Input Sequence in FASTA format

>P42701 (662 residues)
MEPLVTWVVPLLFLFLLSRQGAACRTSECCFQDPPYPDADSGSASGPRDLRCYRISSDRY
ECSWQYEGPTAGVSHFLRCCLSSGRCCYFAAGSATRLQFSDQAGVSVLYTVTLWVESWAR
NQTEKSPEVTLQLYNSVKYEPPLGDIKVSKLAGQLRMEWETPDNQVGAEVQFRHRTPSSP
WKLGDCGPQDDDTESCLCPLEMNVAQEFQLRRRQLGSQGSSWSKWSSPVCVPPENPPQPQ
VRFSVEQLGQDGRRRLTLKEQPTQLELPEGCQGLAPGTEVTYRLQLHMLSCPCKAKATRT
LHLGKMPYLSGAAYNVAVISSNQFGPGLNQTWHIPADTHTEPVALNISVGTNGTTMYWPA
RAQSMTYCIEWQPVGQDGGLATCSLTAPQDPDPAGMATYSWSRESGAMGQEKCYYITIFA
SAHPEKLTLWSTVLSTYHFGGNASAAGTPHHVSVKNHSLDSVSVDWAPSLLSTCPGVLKE
YVVRCRDEDSKQVSEHPVQPTETQVTLSGLRAGVAYTVQVRADTAWLRGVWSQPQRFSIE
VQVSDWLIFFASLGSFLSILLVGVLGYLGLNRAARHLCPPLPTPCASSAIEFPGGKETWQ
WINPVDFQEEASLQEALVVEMSWDKGERTEPLEKTELPEGAPELALDTELSLEDGDRCKA
KM

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	P42701-D1	1-662	662		MEPLVTWVVPLLFLFLLSRQGAACRTSECCFQDPPYPDADSGSASGPRDLRCYRISSDRYECSWQYEGPTAGVSHFLRCCLSSGRCCYFAAGSATRLQFSDQAGVSVLYTVTLWVESWARNQTEKSPEVTLQLYNSVKYEPPLGDIKVSKLAGQLRMEWETPDNQVGAEVQFRHRTPSSPWKLGDCGPQDDDTESCLCPLEMNVAQEFQLRRRQLGSQGSSWSKWSSPVCVPPENPPQPQVRFSVEQLGQDGRRRLTLKEQPTQLELPEGCQGLAPGTEVTYRLQLHMLSCPCKAKATRTLHLGKMPYLSGAAYNVAVISSNQFGPGLNQTWHIPADTHTEPVALNISVGTNGTTMYWPARAQSMTYCIEWQPVGQDGGLATCSLTAPQDPDPAGMATYSWSRESGAMGQEKCYYITIFASAHPEKLTLWSTVLSTYHFGGNASAAGTPHHVSVKNHSLDSVSVDWAPSLLSTCPGVLKEYVVRCRDEDSKQVSEHPVQPTETQVTLSGLRAGVAYTVQVRADTAWLRGVWSQPQRFSIEVQVSDWLIFFASLGSFLSILLVGVLGYLGLNRAARHLCPPLPTPCASSAIEFPGGKETWQWINPVDFQEEASLQEALVVEMSWDKGERTEPLEKTELPEGAPELALDTELSLEDGDRCKAKM

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.404

(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	3l5hA	0.70	3.34	0.146	0.785	model1_3l5hA.pdb.gz
2	3l5iA	0.38	3.28	0.180	0.429	model1_3l5iA.pdb.gz
3	3cmuA	0.36	7.86	0.036	0.570	model1_3cmuA.pdb.gz
4	6um1A	0.36	7.84	0.036	0.567	model1_6um1A.pdb.gz
5	4bujB	0.34	8.38	0.022	0.567	model1_4bujB.pdb.gz
6	2uvcG	0.33	8.48	0.034	0.557	model1_2uvcG.pdb.gz
7	2pffB	0.33	8.37	0.035	0.542	model1_2pffB.pdb.gz
8	7apxA	0.33	8.14	0.045	0.530	model1_7apxA.pdb.gz
9	3qmzA	0.33	8.66	0.044	0.557	model1_3qmzA.pdb.gz
10	5hb4B	0.32	8.15	0.040	0.520	model1_5hb4B.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:0004872	0.89	receptor activity
GO:0038023	0.87	signaling receptor activity
GO:0004888	0.86	transmembrane signaling receptor activity
GO:0004896	0.77	cytokine receptor activity
GO:0005102	0.73	receptor binding
GO:0005126	0.65	cytokine receptor binding
GO:0019955	0.61	cytokine binding
GO:0070851	0.53	growth factor receptor binding
GO:0042020	0.51	interleukin-23 receptor activity
GO:0042019	0.51	interleukin-23 binding
GO:0016517	0.51	interleukin-12 receptor activity
GO:0005143	0.51	interleukin-12 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:0009987	0.97	cellular process
GO:0065007	0.96	biological regulation
GO:0050789	0.96	regulation of biological process
GO:0050794	0.95	regulation of cellular process
GO:0048518	0.89	positive regulation of biological process
GO:0048583	0.87	regulation of response to stimulus
GO:0048522	0.86	positive regulation of cellular process
GO:0051239	0.82	regulation of multicellular organismal process
GO:0051240	0.74	positive regulation of multicellular organismal process
GO:0050896	0.74	response to stimulus
GO:0048584	0.72	positive regulation of response to stimulus
GO:0032101	0.72	regulation of response to external stimulus
GO:0008284	0.71	positive regulation of cell proliferation
GO:0010033	0.63	response to organic substance
GO:0002682	0.63	regulation of immune system process
GO:0001817	0.63	regulation of cytokine production
GO:0071310	0.62	cellular response to organic substance
GO:0050776	0.62	regulation of immune response
GO:0001819	0.62	positive regulation of cytokine production
GO:0050793	0.61	regulation of developmental process
GO:0002684	0.61	positive regulation of immune system process
GO:2000026	0.60	regulation of multicellular organismal development
GO:0080134	0.60	regulation of response to stress
GO:0050870	0.60	positive regulation of T cell activation
GO:0050778	0.60	positive regulation of immune response
GO:0045595	0.60	regulation of cell differentiation
GO:0002825	0.60	regulation of T-helper 1 type immune response
GO:0002697	0.60	regulation of immune effector process
GO:0071346	0.59	cellular response to interferon-gamma
GO:0042104	0.59	positive regulation of activated T cell proliferation
GO:0032729	0.59	positive regulation of interferon-gamma production
GO:0002827	0.59	positive regulation of T-helper 1 type immune response
GO:0002230	0.59	positive regulation of defense response to virus by host
GO:0007165	0.58	signal transduction
GO:0051094	0.51	positive regulation of developmental process
GO:0045597	0.51	positive regulation of cell differentiation

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	0.96	cell part
GO:0044425	0.88	membrane part
GO:0044459	0.87	plasma membrane part
GO:0032991	0.78	macromolecular complex
GO:0043234	0.77	protein complex
GO:0072536	0.71	interleukin-23 receptor complex
GO:0042022	0.71	interleukin-12 receptor complex
GO:0016020	0.58	membrane
GO:0005886	0.53	plasma membrane

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	2pffA	0.270	8.67	0.018	0.461	2.3.1.41 2.3.1.86	NA
2	0.060	1ynnD	0.241	8.51	0.025	0.405	2.7.7.6	NA
3	0.060	2jfdA	0.140	7.40	0.024	0.211	2.3.1.85	NA
4	0.060	3ffzA	0.264	8.00	0.032	0.420	3.4.24.69	NA
5	0.060	3gm8A	0.254	7.62	0.032	0.394	3.2.1.-	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, 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.