D-I-TASSER P19438

D-I-TASSER results for P19438

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

Summary of the Protein

Uniprot ID: P19438
Protein Name: Tumor necrosis factor receptor superfamily member 1A
Gene Name: TNFRSF1A

Input Sequence in FASTA format

>P19438 (455 residues)
MGLSTVPDLLLPLVLLELLVGIYPSGVIGLVPHLGDREKRDSVCPQGKYIHPQNNSICCT
KCHKGTYLYNDCPGPGQDTDCRECESGSFTASENHLRHCLSCSKCRKEMGQVEISSCTVD
RDTVCGCRKNQYRHYWSENLFQCFNCSLCLNGTVHLSCQEKQNTVCTCHAGFFLRENECV
SCSNCKKSLECTKLCLPQIENVKGTEDSGTTVLLPLVIFFGLCLLSLLFIGLMYRYQRWK
SKLYSIVCGKSTPEKEGELEGTTTKPLAPNPSFSPTPGFTPTLGFSPVPSSTFTSSSTYT
PGDCPNFAAPRREVAPPYQGADPILATALASDPIPNPLQKWEDSAHKPQSLDTDDPATLY
AVVENVPPLRWKEFVRRLGLSDHEIDRLELQNGRCLREAQYSMLATWRRRTPRREATLEL
LGRVLRDMDLLGCLEDIEEALCGPAALPPAPSLLR

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	P19438-D1	1-455	455		MGLSTVPDLLLPLVLLELLVGIYPSGVIGLVPHLGDREKRDSVCPQGKYIHPQNNSICCTKCHKGTYLYNDCPGPGQDTDCRECESGSFTASENHLRHCLSCSKCRKEMGQVEISSCTVDRDTVCGCRKNQYRHYWSENLFQCFNCSLCLNGTVHLSCQEKQNTVCTCHAGFFLRENECVSCSNCKKSLECTKLCLPQIENVKGTEDSGTTVLLPLVIFFGLCLLSLLFIGLMYRYQRWKSKLYSIVCGKSTPEKEGELEGTTTKPLAPNPSFSPTPGFTPTLGFSPVPSSTFTSSSTYTPGDCPNFAAPRREVAPPYQGADPILATALASDPIPNPLQKWEDSAHKPQSLDTDDPATLYAVVENVPPLRWKEFVRRLGLSDHEIDRLELQNGRCLREAQYSMLATWRRRTPRREATLELLGRVLRDMDLLGCLEDIEEALCGPAALPPAPSLLR

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.5551

(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	5yz0A	0.40	7.46	0.041	0.675	model1_5yz0A.pdb.gz
2	3javA	0.37	7.82	0.038	0.661	model1_3javA.pdb.gz
3	6yejA	0.35	7.72	0.050	0.620	model1_6yejA.pdb.gz
4	6z2wE	0.35	7.80	0.036	0.620	model1_6z2wE.pdb.gz
5	6qk7A	0.35	6.72	0.044	0.554	model1_6qk7A.pdb.gz
6	6l7eA	0.35	7.59	0.043	0.600	model1_6l7eA.pdb.gz
7	5x6oC	0.34	7.60	0.038	0.600	model1_5x6oC.pdb.gz
8	3hmjA	0.34	7.46	0.045	0.574	model1_3hmjA.pdb.gz
9	6u5vB	0.34	7.93	0.043	0.611	model1_6u5vB.pdb.gz
10	6g7eB	0.33	7.44	0.044	0.567	model1_6g7eB.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	0.97	receptor activity
GO:0005031	0.96	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:0007165	0.93	signal transduction
GO:0006950	0.93	response to stress
GO:0042127	0.92	regulation of cell proliferation
GO:0010033	0.92	response to organic substance
GO:0006952	0.92	defense response
GO:0002376	0.92	immune system process
GO:0032496	0.91	response to lipopolysaccharide
GO:0097190	0.90	apoptotic signaling pathway
GO:0044699	0.90	single-organism process
GO:0006955	0.90	immune response
GO:0006954	0.90	inflammatory response
GO:0032502	0.82	developmental process
GO:0048856	0.81	anatomical structure development
GO:0044767	0.80	single-organism developmental process
GO:0048518	0.76	positive regulation of biological process
GO:0048522	0.74	positive regulation of cellular process
GO:0044707	0.74	single-multicellular organism process
GO:0007275	0.72	multicellular organism development
GO:0080090	0.71	regulation of primary metabolic process
GO:0060255	0.71	regulation of macromolecule metabolic process
GO:0031323	0.70	regulation of cellular metabolic process
GO:0048583	0.69	regulation of response to stimulus
GO:0031325	0.68	positive regulation of cellular metabolic process
GO:0010604	0.68	positive regulation of macromolecule metabolic process
GO:0048584	0.67	positive regulation of response to stimulus
GO:0032268	0.61	regulation of cellular protein metabolic process
GO:0032270	0.60	positive regulation of cellular protein metabolic process
GO:0001932	0.59	regulation of protein phosphorylation
GO:0009966	0.58	regulation of signal transduction
GO:0001934	0.58	positive regulation of protein phosphorylation
GO:1902533	0.57	positive regulation of intracellular signal transduction

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:0044425	0.95	membrane part
GO:0044459	0.94	plasma membrane part
GO:0005887	0.92	integral component of plasma membrane
GO:0044424	0.77	intracellular part
GO:0044444	0.59	cytoplasmic part
GO:0043226	0.55	organelle
GO:0043229	0.54	intracellular organelle
GO:0043227	0.53	membrane-bounded organelle
GO:0043231	0.52	intracellular membrane-bounded organelle

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	3btaA	0.272	7.55	0.045	0.475	3.4.24.69	NA
2	0.060	1nyqB	0.251	6.74	0.062	0.387	6.1.1.3	40
3	0.060	2vz8B	0.293	7.71	0.037	0.519	2.3.1.85	NA
4	0.060	1ug9A	0.260	7.51	0.025	0.444	3.2.1.70	415,439
5	0.060	2vuaA	0.182	7.89	0.044	0.330	3.4.24.69	190,194

	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	3sfzA	0.202	7.41	0.027	0.334	0.15	ADP	complex1.pdb.gz	47,48,65,66,93
2	0.01	3izaA	0.261	7.66	0.022	0.444	0.12	ATP	complex2.pdb.gz	169,171,190,191,192,193
3	0.01	1utcA	0.130	7.12	0.045	0.215	0.18	III	complex3.pdb.gz	47,62,64
4	0.01	1utcA	0.130	7.12	0.045	0.215	0.21	III	complex4.pdb.gz	152,154,168,170
5	0.01	2y0pB	0.207	7.50	0.049	0.354	0.11	ACO	complex5.pdb.gz	47,49,90
6	0.01	3ijeA	0.298	7.26	0.056	0.492	0.28	UUU	complex6.pdb.gz	46,66,68,79,80,82
7	0.01	2xzhA	0.132	6.50	0.019	0.202	0.25	VH2	complex7.pdb.gz	169,172,182
8	0.01	1c9iA	0.141	5.84	0.012	0.204	0.36	III	complex8.pdb.gz	45,46,63,76,78
9	0.01	2uvaG	0.314	7.45	0.030	0.536	0.12	FMN	complex9.pdb.gz	102,103,115
10	0.01	1i1eA	0.279	7.34	0.038	0.468	0.35	DM2	complex10.pdb.gz	64,65,86,87,88,98,99

	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.