D-I-TASSER P36941

D-I-TASSER results for P36941

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

Summary of the Protein

Uniprot ID: P36941
Protein Name: Tumor necrosis factor receptor superfamily member 3
Gene Name: LTBR

Input Sequence in FASTA format

>P36941 (435 residues)
MLLPWATSAPGLAWGPLVLGLFGLLAASQPQAVPPYASENQTCRDQEKEYYEPQHRICCS
RCPPGTYVSAKCSRIRDTVCATCAENSYNEHWNYLTICQLCRPCDPVMGLEEIAPCTSKR
KTQCRCQPGMFCAAWALECTHCELLSDCPPGTEAELKDEVGKGNNHCVPCKAGHFQNTSS
PSARCQPHTRCENQGLVEAAPGTAQSDTTCKNPLEPLPPEMSGTMLMLAVLLPLAFFLLL
ATVFSCIWKSHPSLCRKLGSLLKRRPQGEGPNPVAGSWEPPKAHPYFPDLVQPLLPISGD
VSPVSTGLPAAPVLEAGVPQQQSPLDLTREPQLEPGEQSQVAHGTNGIHVTGGSMTITGN
IYIYNGPVLGGPPGPGDLPATPEPPYPIPEEGDPGPPGLSTPHQEDGKAWHLAETEHCGA
TPSNRGPRNQFITHD

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	P36941-D1	1-435	435		MLLPWATSAPGLAWGPLVLGLFGLLAASQPQAVPPYASENQTCRDQEKEYYEPQHRICCSRCPPGTYVSAKCSRIRDTVCATCAENSYNEHWNYLTICQLCRPCDPVMGLEEIAPCTSKRKTQCRCQPGMFCAAWALECTHCELLSDCPPGTEAELKDEVGKGNNHCVPCKAGHFQNTSSPSARCQPHTRCENQGLVEAAPGTAQSDTTCKNPLEPLPPEMSGTMLMLAVLLPLAFFLLLATVFSCIWKSHPSLCRKLGSLLKRRPQGEGPNPVAGSWEPPKAHPYFPDLVQPLLPISGDVSPVSTGLPAAPVLEAGVPQQQSPLDLTREPQLEPGEQSQVAHGTNGIHVTGGSMTITGNIYIYNGPVLGGPPGPGDLPATPEPPYPIPEEGDPGPPGLSTPHQEDGKAWHLAETEHCGATPSNRGPRNQFITHD

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.5568

(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	6w1sI	0.40	6.80	0.046	0.639	model1_6w1sI.pdb.gz
2	5yz0A	0.39	7.02	0.045	0.632	model1_5yz0A.pdb.gz
3	2pffB	0.39	7.25	0.036	0.651	model1_2pffB.pdb.gz
4	5fvmA	0.38	7.07	0.033	0.623	model1_5fvmA.pdb.gz
5	5u1sA	0.37	7.33	0.032	0.623	model1_5u1sA.pdb.gz
6	6zwmA	0.36	6.84	0.029	0.575	model1_6zwmA.pdb.gz
7	3qmzA	0.36	6.76	0.031	0.570	model1_3qmzA.pdb.gz
8	6v3fA	0.36	6.91	0.050	0.572	model1_6v3fA.pdb.gz
9	5h64A	0.35	7.26	0.036	0.586	model1_5h64A.pdb.gz
10	5ijoJ	0.35	7.46	0.050	0.595	model1_5ijoJ.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:0005031	0.97	tumor necrosis factor-activated receptor activity

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:0050794	0.99	regulation of cellular process
GO:0042981	0.96	regulation of apoptotic process
GO:0050896	0.94	response to stimulus
GO:0043207	0.93	response to external biotic stimulus
GO:0006952	0.93	defense response
GO:0042127	0.92	regulation of cell proliferation
GO:0032496	0.92	response to lipopolysaccharide
GO:0007165	0.92	signal transduction
GO:0002376	0.92	immune system process
GO:0044699	0.91	single-organism process
GO:0006954	0.91	inflammatory response
GO:0006955	0.90	immune response
GO:0097190	0.88	apoptotic signaling pathway
GO:0048856	0.88	anatomical structure development
GO:0044767	0.86	single-organism developmental process
GO:0048518	0.84	positive regulation of biological process
GO:0048522	0.81	positive regulation of cellular process
GO:0080090	0.79	regulation of primary metabolic process
GO:0060255	0.79	regulation of macromolecule metabolic process
GO:0032501	0.79	multicellular organismal process
GO:0044707	0.78	single-multicellular organism process
GO:0031323	0.78	regulation of cellular metabolic process
GO:0048583	0.77	regulation of response to stimulus
GO:0031325	0.77	positive regulation of cellular metabolic process
GO:0010604	0.77	positive regulation of macromolecule metabolic process
GO:0007275	0.77	multicellular organism development
GO:0051246	0.76	regulation of protein metabolic process
GO:0048584	0.76	positive regulation of response to stimulus
GO:0032270	0.74	positive regulation of cellular protein metabolic process
GO:0009966	0.73	regulation of signal transduction
GO:0001934	0.73	positive regulation of protein phosphorylation
GO:1902533	0.72	positive regulation of intracellular signal transduction
GO:0043410	0.70	positive regulation of MAPK cascade

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:0044459	0.97	plasma membrane part
GO:0031226	0.95	intrinsic component of plasma membrane
GO:0016021	0.95	integral component of membrane
GO:0005887	0.94	integral component of plasma membrane
GO:0044424	0.55	intracellular part

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	2vkzG	0.351	7.03	0.039	0.572	2.3.1.38 3.1.2.14	NA
2	0.060	1e6yA	0.238	7.36	0.027	0.407	2.8.4.1	NA
3	0.060	2j5wA	0.243	6.41	0.033	0.377	1.16.3.1	NA
4	0.060	2wghB	0.242	6.86	0.061	0.391	1.17.4.1	185
5	0.060	3b43A	0.257	7.03	0.031	0.414	2.7.11.1	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:

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	3cmvD	0.231	7.05	0.036	0.384	0.17	ANP	complex1.pdb.gz	110,127,128,129,147,164
2	0.01	1lvkA	0.212	6.29	0.034	0.322	0.19	UUU	complex2.pdb.gz	149,150,151,152,153,154,176,177,178,179
3	0.01	1vomA	0.222	6.76	0.037	0.347	0.11	UUU	complex3.pdb.gz	172,173,174,175,176
4	0.01	3cmvE	0.206	7.15	0.027	0.347	0.11	ANP	complex4.pdb.gz	149,150,151,173,177
5	0.01	3cmvG	0.210	7.62	0.044	0.370	0.13	ANP	complex5.pdb.gz	127,128,129,147,164
6	0.01	3bz9A	0.217	6.69	0.027	0.338	0.29	BL7	complex6.pdb.gz	170,174,175,176
7	0.01	3cmvA	0.219	7.50	0.025	0.377	0.16	ANP	complex7.pdb.gz	107,111,129
8	0.01	3bz7A	0.218	6.51	0.021	0.333	0.21	BL4	complex8.pdb.gz	105,106,108,129
9	0.01	1yv3A	0.218	6.95	0.024	0.349	0.18	BIT	complex9.pdb.gz	129,130,131
10	0.01	3cmvA	0.219	7.50	0.025	0.377	0.18	ANP	complex10.pdb.gz	148,149,150,151,152

	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.