D-I-TASSER P0DP04

D-I-TASSER results for P0DP04

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

Summary of the Protein

Uniprot ID: P0DP04
Protein Name: Immunoglobulin heavy variable 3-43D
Gene Name: IGHV3-43D

Input Sequence in FASTA format

>P0DP04 (118 residues)
MEFGLSWVFLVAILKGVQCEVQLVESGGVVVQPGGSLRLSCAASGFTFDDYAMHWVRQAP
GKGLEWVSLISWDGGSTYYADSVKGRFTISRDNSKNSLYLQMNSLRAEDTALYYCAKD

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	P0DP04-D1	1-118	118		MEFGLSWVFLVAILKGVQCEVQLVESGGVVVQPGGSLRLSCAASGFTFDDYAMHWVRQAPGKGLEWVSLISWDGGSTYYADSVKGRFTISRDNSKNSLYLQMNSLRAEDTALYYCAKD

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.7884

(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	6wznA	0.86	1.95	0.704	0.941	model1_6wznA.pdb.gz
2	4rrpA	0.85	2.18	0.675	0.941	model1_4rrpA.pdb.gz
3	3ux9B	0.85	1.90	0.757	0.924	model1_3ux9B.pdb.gz
4	3wbdA	0.84	1.96	0.409	0.941	model1_3wbdA.pdb.gz
5	6lfvA	0.84	2.18	0.596	0.932	model1_6lfvA.pdb.gz
6	6k4zA	0.84	2.01	0.426	0.949	model1_6k4zA.pdb.gz
7	2gjjA	0.83	2.00	0.348	0.932	model1_2gjjA.pdb.gz
8	4yjzL	0.83	2.16	0.439	0.941	model1_4yjzL.pdb.gz
9	1x9qA	0.83	2.06	0.561	0.941	model1_1x9qA.pdb.gz
10	1qgc4	0.83	2.05	0.600	0.924	model1_1qgc4.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:0003823	0.97	antigen binding
GO:0005102	0.88	receptor binding
GO:0034987	0.87	immunoglobulin receptor binding
GO:0004252	0.52	serine-type endopeptidase 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:0050896	1.00	response to stimulus
GO:0006955	0.99	immune response
GO:0045087	0.84	innate immune response
GO:0044699	0.84	single-organism process
GO:0065007	0.80	biological regulation
GO:0006958	0.79	complement activation, classical pathway
GO:0002429	0.79	immune response-activating cell surface receptor signaling pathway
GO:0043207	0.71	response to external biotic stimulus
GO:0050871	0.70	positive regulation of B cell activation
GO:0050853	0.70	B cell receptor signaling pathway
GO:0042742	0.70	defense response to bacterium
GO:0006911	0.70	phagocytosis, engulfment
GO:0006910	0.70	phagocytosis, recognition

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:0005576	0.95	extracellular region
GO:0044421	0.92	extracellular region part
GO:0044464	0.83	cell part
GO:0044459	0.73	plasma membrane part
GO:0072562	0.72	blood microparticle
GO:0042571	0.71	immunoglobulin complex, circulating
GO:0009897	0.71	external side of 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	0.341	1zv5A	0.748	1.73	0.680	0.822	3.2.1.17	26,28,38,40,89,99,101,114
2	0.336	1zvhA	0.777	1.43	0.657	0.839	3.2.1.17	23,25,28,58,112,114
3	0.319	1ri8A	0.763	1.33	0.649	0.822	3.2.1.17	23,25,28,114
4	0.067	2eo1A	0.554	2.38	0.145	0.661	2.7.11.1	62,64,107
5	0.067	2bk8A	0.582	1.72	0.128	0.661	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	0.11	3ffdA	0.808	0.94	0.717	0.839	1.16	III	complex1.pdb.gz	50,71,72,73,74,75,76,78,118
2	0.11	3dsfH	0.809	0.87	0.717	0.839	0.53	III	complex2.pdb.gz	91,92,95
3	0.10	1indH	0.792	1.13	0.677	0.839	0.74	EOT	complex3.pdb.gz	57,62,64
4	0.05	1himH	0.683	1.72	0.286	0.771	0.52	III	complex4.pdb.gz	58,59,60,62,64
5	0.04	1iai0	0.675	1.81	0.275	0.771	0.58	III	complex5.pdb.gz	28,35,36,38,97
6	0.04	1jhk0	0.678	1.71	0.267	0.763	0.51	III	complex6.pdb.gz	56,58,63,64,66,69,79,80,114
7	0.04	3ietA	0.689	1.55	0.256	0.763	0.51	III	complex7.pdb.gz	58,60,63,65
8	0.04	1kn4L	0.700	1.51	0.220	0.771	0.53	PDE	complex8.pdb.gz	56,58,61,64,66

	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.