D-I-TASSER P02753

D-I-TASSER results for P02753

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Summary of the Protein

Uniprot ID: P02753
Protein Name: Retinol-binding protein 4
Gene Name: RBP4

Input Sequence in FASTA format

>P02753 (201 residues)
MKWVWALLLLAALGSGRAERDCRVSSFRVKENFDKARFSGTWYAMAKKDPEGLFLQDNIV
AEFSVDETGQMSATAKGRVRLLNNWDVCADMVGTFTDTEDPAKFKMKYWGVASFLQKGND
DHWIVDTDYDTYAVQYSCRLLNLDGTCADSYSFVFSRDPNGLPPEAQKIVRQRQEELCLA
RQYRLIVHNGYCDGRSERNLL

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	P02753-D1	1-201	201		MKWVWALLLLAALGSGRAERDCRVSSFRVKENFDKARFSGTWYAMAKKDPEGLFLQDNIVAEFSVDETGQMSATAKGRVRLLNNWDVCADMVGTFTDTEDPAKFKMKYWGVASFLQKGNDDHWIVDTDYDTYAVQYSCRLLNLDGTCADSYSFVFSRDPNGLPPEAQKIVRQRQEELCLARQYRLIVHNGYCDGRSERNLL

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.9461

(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	1aqbA	0.86	0.44	0.937	0.871	model1_1aqbA.pdb.gz
2	1qabE	0.84	1.62	0.967	0.881	model1_1qabE.pdb.gz
3	5ez2A	0.69	2.35	0.227	0.786	model1_5ez2A.pdb.gz
4	1i4uA	0.68	2.66	0.187	0.801	model1_1i4uA.pdb.gz
5	1gkaB	0.68	2.42	0.189	0.786	model1_1gkaB.pdb.gz
6	1z24A	0.67	3.05	0.177	0.816	model1_1z24A.pdb.gz
7	2hzqA	0.65	3.03	0.220	0.781	model1_2hzqA.pdb.gz
8	2qosC	0.64	3.23	0.198	0.771	model1_2qosC.pdb.gz
9	1epbB	0.63	2.67	0.204	0.731	model1_1epbB.pdb.gz
10	3ebwA	0.62	2.78	0.151	0.741	model1_3ebwA.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:0043178	0.98	alcohol binding
GO:0008289	0.98	lipid binding
GO:0097159	0.60	organic cyclic compound binding
GO:0005496	0.55	steroid binding
GO:0015485	0.54	cholesterol binding
GO:0005215	0.50	transporter 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:0044699	0.94	single-organism process
GO:0048856	0.90	anatomical structure development
GO:0042221	0.90	response to chemical
GO:1901700	0.89	response to oxygen-containing compound
GO:0009987	0.88	cellular process
GO:0008152	0.88	metabolic process
GO:0071704	0.86	organic substance metabolic process
GO:0044238	0.86	primary metabolic process
GO:0044763	0.85	single-organism cellular process
GO:0044710	0.85	single-organism metabolic process
GO:0065007	0.84	biological regulation
GO:0006629	0.83	lipid metabolic process
GO:0044767	0.81	single-organism developmental process
GO:0044281	0.81	small molecule metabolic process
GO:0048513	0.80	animal organ development
GO:0050789	0.76	regulation of biological process
GO:0050794	0.74	regulation of cellular process
GO:0044723	0.71	single-organism carbohydrate metabolic process
GO:0051223	0.70	regulation of protein transport
GO:0023051	0.70	regulation of signaling
GO:0010646	0.70	regulation of cell communication
GO:0006006	0.70	glucose metabolic process
GO:0002682	0.64	regulation of immune system process
GO:0051239	0.63	regulation of multicellular organismal process
GO:0048523	0.63	negative regulation of cellular process
GO:0009888	0.63	tissue development
GO:0051241	0.62	negative regulation of multicellular organismal process
GO:0008285	0.62	negative regulation of cell proliferation
GO:0044237	0.55	cellular metabolic process
GO:0016043	0.53	cellular component organization
GO:0048589	0.52	developmental growth

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:0005615	1.00	extracellular space
GO:0044464	0.93	cell part
GO:0044424	0.91	intracellular part
GO:0044444	0.87	cytoplasmic part
GO:0043227	0.73	membrane-bounded organelle
GO:0043231	0.56	intracellular membrane-bounded organelle
GO:0032991	0.53	macromolecular complex

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	1ye9K	0.290	4.08	0.022	0.413	1.11.1.6	73,92
2	0.060	1sy7A	0.413	5.46	0.051	0.672	1.11.1.6	NA
3	0.060	1qwlA	0.429	4.65	0.072	0.622	1.11.1.6	NA
4	0.060	1m7sD	0.406	5.37	0.044	0.662	1.11.1.6	NA
5	0.060	1yq2A	0.420	5.17	0.041	0.667	3.2.1.23	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	0.94	1rbpA	0.859	0.49	1.000	0.866	1.96	RTL	complex1.pdb.gz	53,54,61,73,75,79,81,91,106,116,122,153
2	0.94	2wqaE	0.868	0.53	1.000	0.876	1.81	OLA	complex2.pdb.gz	47,50,53,54,55,63,73,75,91,92,93,106,108,122,151,153,155
3	0.92	1qabF	0.830	0.88	0.982	0.851	1.90	RTL	complex3.pdb.gz	53,54,73,75,91,92,93,106,108,115,116
4	0.87	1qabE	0.835	1.62	0.967	0.881	1.68	RTL	complex4.pdb.gz	54,55,63,75,91,106,108,115,122
5	0.31	2hzqA	0.664	2.87	0.217	0.786	1.09	STR	complex5.pdb.gz	61,63,75,108,123,153,155
6	0.25	3uexA	0.629	2.66	0.188	0.736	0.86	STE	complex6.pdb.gz	35,63,71,77,93,106,122,124,135,137
7	0.24	1z24A	0.672	3.05	0.177	0.816	0.81	BLV	complex7.pdb.gz	44,50,59,60,75,76,77,91,106,120,137,151,153,155
8	0.22	1n0sA	0.647	3.16	0.173	0.786	0.81	FLU	complex8.pdb.gz	37,63,74,91,106,120,122,151,153
9	0.09	1epbA	0.616	2.63	0.203	0.716	0.96	REA	complex9.pdb.gz	35,38,42,61,63,120,122,124,133,135,137,153,155
10	0.04	1gkaB	0.683	2.42	0.189	0.786	0.83	AXT	complex10.pdb.gz	44,50,75,93,105,107,121,137,146,148,151,153

	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.