D-I-TASSER P29965

D-I-TASSER results for P29965

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

Summary of the Protein

Uniprot ID: P29965
Protein Name: CD40 ligand
Gene Name: CD40LG

Input Sequence in FASTA format

>P29965 (261 residues)
MIETYNQTSPRSAATGLPISMKIFMYLLTVFLITQMIGSALFAVYLHRRLDKIEDERNLH
EDFVFMKTIQRCNTGERSLSLLNCEEIKSQFEGFVKDIMLNKEETKKENSFEMQKGDQNP
QIAAHVISEASSKTTSVLQWAEKGYYTMSNNLVTLENGKQLTVKRQGLYYIYAQVTFCSN
REASSQAPFIASLCLKSPGRFERILLRAANTHSSAKPCGQQSIHLGGVFELQPGASVFVN
VTDPSQVSHGTGFTSFGLLKL

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	P29965-D1	1-120	120		MIETYNQTSPRSAATGLPISMKIFMYLLTVFLITQMIGSALFAVYLHRRLDKIEDERNLHEDFVFMKTIQRCNTGERSLSLLNCEEIKSQFEGFVKDIMLNKEETKKENSFEMQKGDQNP
2	P29965-D2	121-261	141		QIAAHVISEASSKTTSVLQWAEKGYYTMSNNLVTLENGKQLTVKRQGLYYIYAQVTFCSNREASSQAPFIASLCLKSPGRFERILLRAANTHSSAKPCGQQSIHLGGVFELQPGASVFVNVTDPSQVSHGTGFTSFGLLKL

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.64

(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	1i9rA	0.54	0.97	1.000	0.548	model1_1i9rA.pdb.gz
2	2re9A	0.51	2.24	0.264	0.552	model1_2re9A.pdb.gz
3	4msvA	0.49	1.67	0.243	0.521	model1_4msvA.pdb.gz
4	1d4vB	0.49	2.16	0.237	0.533	model1_1d4vB.pdb.gz
5	1s55A	0.49	2.07	0.266	0.533	model1_1s55A.pdb.gz
6	1tnrA	0.48	2.08	0.228	0.521	model1_1tnrA.pdb.gz
7	1otzx	0.47	1.65	0.189	0.506	model1_1otzx.pdb.gz
8	3ugnA	0.47	2.34	0.255	0.525	model1_3ugnA.pdb.gz
9	4mxwY	0.46	1.71	0.268	0.487	model1_4mxwY.pdb.gz
10	4ht1T	0.44	2.38	0.227	0.490	model1_4ht1T.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:0005102	1.00	receptor binding
GO:0032813	0.97	tumor necrosis factor receptor superfamily binding
GO:0005174	0.89	CD40 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:0050794	0.98	regulation of cellular process
GO:0048518	0.81	positive regulation of biological process
GO:0048522	0.78	positive regulation of cellular process
GO:0019222	0.75	regulation of metabolic process
GO:0060255	0.74	regulation of macromolecule metabolic process
GO:0031323	0.74	regulation of cellular metabolic process
GO:0080090	0.73	regulation of primary metabolic process
GO:0048583	0.72	regulation of response to stimulus
GO:0010604	0.72	positive regulation of macromolecule metabolic process
GO:0051246	0.71	regulation of protein metabolic process
GO:0048584	0.71	positive regulation of response to stimulus
GO:0031325	0.71	positive regulation of cellular metabolic process
GO:0051247	0.70	positive regulation of protein metabolic process
GO:0044699	0.70	single-organism process
GO:0009987	0.70	cellular process
GO:0009967	0.70	positive regulation of signal transduction
GO:0065009	0.68	regulation of molecular function
GO:0032270	0.68	positive regulation of cellular protein metabolic process
GO:0043085	0.67	positive regulation of catalytic activity
GO:1902533	0.66	positive regulation of intracellular signal transduction
GO:0080134	0.65	regulation of response to stress
GO:0001934	0.65	positive regulation of protein phosphorylation
GO:0043406	0.64	positive regulation of MAP kinase activity
GO:0044763	0.63	single-organism cellular process
GO:0043507	0.63	positive regulation of JUN kinase activity
GO:0050896	0.60	response to stimulus
GO:0051239	0.57	regulation of multicellular organismal process
GO:0002376	0.57	immune system process
GO:0031326	0.56	regulation of cellular biosynthetic process
GO:0010556	0.56	regulation of macromolecule biosynthetic process
GO:0010468	0.55	regulation of gene expression
GO:0051240	0.54	positive regulation of multicellular organismal process
GO:0019219	0.54	regulation of nucleobase-containing compound metabolic process
GO:0007165	0.54	signal transduction
GO:0002682	0.54	regulation of immune system process
GO:0006355	0.53	regulation of transcription, DNA-templated
GO:0002684	0.53	positive regulation of immune system process
GO:0006950	0.52	response to stress
GO:0001817	0.52	regulation of cytokine production
GO:0006952	0.51	defense response
GO:0001819	0.51	positive regulation of cytokine production
GO:0001775	0.51	cell activation
GO:1903039	0.50	positive regulation of leukocyte cell-cell adhesion
GO:0045321	0.50	leukocyte activation

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:0009986	0.84	cell surface

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	2cseA	0.406	4.95	0.017	0.586	2.7.7.50	NA
2	0.060	1ev11	0.368	5.17	0.076	0.552	3.4.22.28	NA
3	0.060	2np0A	0.411	5.42	0.025	0.644	3.4.24.69	NA
4	0.060	3l4uA	0.393	5.12	0.051	0.594	3.2.1.20 3.2.1.3	159,224
5	0.060	2vuaA	0.321	4.70	0.040	0.467	3.4.24.69	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	0.44	3lkjA	0.496	1.13	0.992	0.510	1.84	LKJ	complex1.pdb.gz	168,170,228,230,259,261
2	0.44	3lkjC	0.475	1.40	0.992	0.494	1.90	LKJ	complex2.pdb.gz	121,123,125,145,170,172,224,225,259,261
3	0.10	2az5B	0.484	1.86	0.281	0.517	1.44	307	complex3.pdb.gz	170,172,224,225,226,255
4	0.04	1oqd0	0.475	1.66	0.189	0.506	1.07	III	complex4.pdb.gz	121,168,204,205,206,207,208,209,210,211,224,225,226,228,261
5	0.04	1oqd5	0.475	1.66	0.189	0.506	0.97	III	complex5.pdb.gz	120,121,125,147,149,174,209,212,215,220,221,222,224,252,253,255,259
6	0.03	3k48A	0.468	1.84	0.189	0.506	0.83	III	complex6.pdb.gz	176,177,178,219,246,247,248,251

	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.