D-I-TASSER P24593

D-I-TASSER results for P24593

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

Summary of the Protein

Uniprot ID: P24593
Protein Name: Insulin-like growth factor-binding protein 5
Gene Name: IGFBP5

Input Sequence in FASTA format

>P24593 (272 residues)
MVLLTAVLLLLAAYAGPAQSLGSFVHCEPCDEKALSMCPPSPLGCELVKEPGCGCCMTCA
LAEGQSCGVYTERCAQGLRCLPRQDEEKPLHALLHGRGVCLNEKSYREQVKIERDSREHE
EPTTSEMAEETYSPKIFRPKHTRISELKAEAVKKDRRKKLTQSKFVGGAENTAHPRIISA
PEMRQESEQGPCRRHMEASLQELKASPRMVPRAVYLPNCDRKGFYKRKQCKPSRGRKRGI
CWCVDKYGMKLPGMEYVDGDFQCHTFDSSNVE

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	P24593-D1	1-272	272		MVLLTAVLLLLAAYAGPAQSLGSFVHCEPCDEKALSMCPPSPLGCELVKEPGCGCCMTCALAEGQSCGVYTERCAQGLRCLPRQDEEKPLHALLHGRGVCLNEKSYREQVKIERDSREHEEPTTSEMAEETYSPKIFRPKHTRISELKAEAVKKDRRKKLTQSKFVGGAENTAHPRIISAPEMRQESEQGPCRRHMEASLQELKASPRMVPRAVYLPNCDRKGFYKRKQCKPSRGRKRGICWCVDKYGMKLPGMEYVDGDFQCHTFDSSNVE

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.3634

(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	5zakA	0.45	6.48	0.047	0.794	model1_5zakA.pdb.gz
2	2zxqA	0.42	6.53	0.052	0.768	model1_2zxqA.pdb.gz
3	5yfbA	0.42	6.33	0.046	0.721	model1_5yfbA.pdb.gz
4	3jc5c	0.42	6.07	0.051	0.713	model1_3jc5c.pdb.gz
5	3abzA	0.41	6.43	0.033	0.739	model1_3abzA.pdb.gz
6	3efmA	0.41	6.01	0.069	0.676	model1_3efmA.pdb.gz
7	6e4vA	0.40	6.05	0.048	0.676	model1_6e4vA.pdb.gz
8	2w78A2	0.40	6.21	0.039	0.691	model1_2w78A2.pdb.gz
9	2d5wA	0.40	6.42	0.042	0.710	model1_2d5wA.pdb.gz
10	4zgvA	0.40	5.91	0.047	0.654	model1_4zgvA.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:0005520	0.96	insulin-like growth factor binding
GO:0031995	0.94	insulin-like growth factor II binding
GO:0031994	0.94	insulin-like growth factor I 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:0065007	0.73	biological regulation
GO:0050789	0.72	regulation of biological process
GO:0050794	0.68	regulation of cellular process
GO:0050896	0.67	response to stimulus
GO:0042221	0.64	response to chemical
GO:0010033	0.63	response to organic substance
GO:0009719	0.63	response to endogenous stimulus
GO:0009725	0.62	response to hormone
GO:1901700	0.61	response to oxygen-containing compound
GO:0010243	0.61	response to organonitrogen compound
GO:0043434	0.60	response to peptide hormone
GO:0048583	0.55	regulation of response to stimulus
GO:0023051	0.54	regulation of signaling
GO:0010646	0.54	regulation of cell communication
GO:0009966	0.53	regulation of signal transduction
GO:0060416	0.50	response to growth hormone
GO:0043567	0.50	regulation of insulin-like growth factor receptor signaling pathway

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:0044421	0.96	extracellular region part
GO:0005615	0.92	extracellular space
GO:0044464	0.54	cell 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	1bxrA	0.374	6.60	0.034	0.688	6.3.5.5	249
2	0.060	3g0bB	0.372	6.21	0.071	0.643	3.4.14.5	216
3	0.060	1k32A	0.350	6.18	0.045	0.603	3.4.21.-	NA
4	0.060	1h54B	0.380	5.85	0.050	0.618	2.4.1.8	NA
5	0.060	1ofdA	0.356	6.58	0.041	0.640	1.4.7.1	14

	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	2ckjA	0.311	6.68	0.031	0.577	0.69	FES	complex1.pdb.gz	61,62,63,64,65,67,80
2	0.01	1v97A	0.363	6.16	0.042	0.621	0.62	FES	complex2.pdb.gz	190,192,194,196,219,220,222
3	0.01	2ckjB	0.356	6.15	0.042	0.610	0.62	FES	complex3.pdb.gz	217,218,219,225,227,228
4	0.01	1fo4A	0.362	6.19	0.047	0.618	0.62	FES	complex4.pdb.gz	189,190,191,193,219,220,221
5	0.01	1fiqA	0.162	6.49	0.042	0.290	0.69	FES	complex5.pdb.gz	189,190,192,220,222
6	0.01	2ckjD	0.325	6.41	0.022	0.581	0.66	FES	complex6.pdb.gz	230,231,233,239,240,241
7	0.01	2ckjA	0.311	6.68	0.031	0.577	0.84	FES	complex7.pdb.gz	189,190,191,193,219,220,221,222

	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.