D-I-TASSER Q9UBN6

D-I-TASSER results for Q9UBN6

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

Summary of the Protein

Uniprot ID: Q9UBN6
Protein Name: Tumor necrosis factor receptor superfamily member 10D
Gene Name: TNFRSF10D

Input Sequence in FASTA format

>Q9UBN6 (386 residues)
MGLWGQSVPTASSARAGRYPGARTASGTRPWLLDPKILKFVVFIVAVLLPVRVDSATIPR
QDEVPQQTVAPQQQRRSLKEEECPAGSHRSEYTGACNPCTEGVDYTIASNNLPSCLLCTV
CKSGQTNKSSCTTTRDTVCQCEKGSFQDKNSPEMCRTCRTGCPRGMVKVSNCTPRSDIKC
KNESAASSTGKTPAAEETVTTILGMLASPYHYLIIIVVLVIILAVVVVGFSCRKKFISYL
KGICSGGGGGPERVHRVLFRRRSCPSRVPGAEDNARNETLSNRYLQPTQVSEQEIQGQEL
AELTGVTVESPEEPQRLLEQAEAEGCQRRRLLVPVNDADSADISTLLDASATLEEGHAKE
TIQDQLVGSEKLFYEEDEAGSATSCL

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	Q9UBN6-D1	1-386	386		MGLWGQSVPTASSARAGRYPGARTASGTRPWLLDPKILKFVVFIVAVLLPVRVDSATIPRQDEVPQQTVAPQQQRRSLKEEECPAGSHRSEYTGACNPCTEGVDYTIASNNLPSCLLCTVCKSGQTNKSSCTTTRDTVCQCEKGSFQDKNSPEMCRTCRTGCPRGMVKVSNCTPRSDIKCKNESAASSTGKTPAAEETVTTILGMLASPYHYLIIIVVLVIILAVVVVGFSCRKKFISYLKGICSGGGGGPERVHRVLFRRRSCPSRVPGAEDNARNETLSNRYLQPTQVSEQEIQGQELAELTGVTVESPEEPQRLLEQAEAEGCQRRRLLVPVNDADSADISTLLDASATLEEGHAKETIQDQLVGSEKLFYEEDEAGSATSCL

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.5593

(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	5hb4B	0.44	6.13	0.050	0.668	model1_5hb4B.pdb.gz
2	6yejA	0.41	6.96	0.039	0.689	model1_6yejA.pdb.gz
3	5u1sA	0.39	6.71	0.045	0.629	model1_5u1sA.pdb.gz
4	3thwB	0.37	6.67	0.035	0.611	model1_3thwB.pdb.gz
5	6zwmA	0.37	7.10	0.026	0.629	model1_6zwmA.pdb.gz
6	6edoA	0.37	6.95	0.030	0.624	model1_6edoA.pdb.gz
7	2o8cB	0.36	6.59	0.033	0.578	model1_2o8cB.pdb.gz
8	1nneA	0.36	6.92	0.047	0.593	model1_1nneA.pdb.gz
9	6mzbB	0.36	6.57	0.044	0.557	model1_6mzbB.pdb.gz
10	6zymA	0.35	6.42	0.037	0.570	model1_6zymA.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	0.96	receptor activity
GO:0005031	0.95	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:0050896	0.94	response to stimulus
GO:0042981	0.94	regulation of apoptotic process
GO:0044699	0.92	single-organism process
GO:0009605	0.92	response to external stimulus
GO:0006952	0.92	defense response
GO:0043207	0.91	response to external biotic stimulus
GO:0042127	0.91	regulation of cell proliferation
GO:0007165	0.91	signal transduction
GO:0010033	0.90	response to organic substance
GO:0002376	0.90	immune system process
GO:0097190	0.89	apoptotic signaling pathway
GO:0032496	0.89	response to lipopolysaccharide
GO:0006955	0.89	immune response
GO:0006954	0.89	inflammatory response
GO:0032502	0.86	developmental process
GO:0048856	0.85	anatomical structure development
GO:0044767	0.85	single-organism developmental process
GO:0032501	0.77	multicellular organismal process
GO:0044707	0.76	single-multicellular organism process
GO:0007275	0.75	multicellular organism development
GO:0007166	0.62	cell surface receptor signaling pathway
GO:0008625	0.59	extrinsic apoptotic signaling pathway via death domain receptors
GO:0048518	0.58	positive regulation of biological process
GO:0048522	0.56	positive regulation of cellular process
GO:0060255	0.53	regulation of macromolecule metabolic process
GO:0080090	0.52	regulation of primary metabolic process
GO:0031323	0.52	regulation of cellular metabolic process
GO:0048583	0.50	regulation of response to stimulus
GO:0031325	0.50	positive regulation of cellular metabolic process
GO:0010604	0.50	positive regulation of macromolecule metabolic 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:0044464	0.99	cell part
GO:0044459	0.95	plasma membrane part
GO:0031226	0.92	intrinsic component of plasma membrane
GO:0016021	0.92	integral component of membrane
GO:0005887	0.91	integral component of plasma membrane
GO:0044424	0.66	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	3l4uA	0.311	6.56	0.053	0.497	3.2.1.20 3.2.1.3	NA
2	0.060	1w9xA	0.278	7.11	0.045	0.477	3.2.1.1	NA
3	0.060	3eqoA	0.223	6.50	0.044	0.355	3.2.1.58	NA
4	0.060	2hwgA	0.256	6.46	0.079	0.396	2.7.3.9	NA
5	0.060	2pffA	0.309	7.29	0.060	0.541	2.3.1.41 2.3.1.86	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	1mneA	0.209	6.95	0.021	0.352	0.48	POP	complex1.pdb.gz	86,87,99,100,116,117

	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.