D-I-TASSER P02774

D-I-TASSER results for P02774

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

Summary of the Protein

Uniprot ID: P02774
Protein Name: Vitamin D-binding protein
Gene Name: GC

Input Sequence in FASTA format

>P02774 (474 residues)
MKRVLVLLLAVAFGHALERGRDYEKNKVCKEFSHLGKEDFTSLSLVLYSRKFPSGTFEQV
SQLVKEVVSLTEACCAEGADPDCYDTRTSALSAKSCESNSPFPVHPGTAECCTKEGLERK
LCMAALKHQPQEFPTYVEPTNDEICEAFRKDPKEYANQFMWEYSTNYGQAPLSLLVSYTK
SYLSMVGSCCTSASPTVCFLKERLQLKHLSLLTTLSNRVCSQYAAYGEKKSRLSNLIKLA
QKVPTADLEDVLPLAEDITNILSKCCESASEDCMAKELPEHTVKLCDNLSTKNSKFEDCC
QEKTAMDVFVCTYFMPAAQLPELPDVELPTNKDVCDPGNTKVMDKYTFELSRRTHLPEVF
LSKVLEPTLKSLGECCDVEDSTTCFNAKGPLLKKELSSFIDKGQELCADYSENTFTEYKK
KLAERLKAKLPDATPTELAKLVNKHSDFASNCCSINSPPLYCDSEIDAELKNIL

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	P02774-D1	1-131	131		MKRVLVLLLAVAFGHALERGRDYEKNKVCKEFSHLGKEDFTSLSLVLYSRKFPSGTFEQVSQLVKEVVSLTEACCAEGADPDCYDTRTSALSAKSCESNSPFPVHPGTAECCTKEGLERKLCMAALKHQPQ
2	P02774-D2	132-205	74		EFPTYVEPTNDEICEAFRKDPKEYANQFMWEYSTNYGQAPLSLLVSYTKSYLSMVGSCCTSASPTVCFLKERLQ
3	P02774-D3	206-321	116		LKHLSLLTTLSNRVCSQYAAYGEKKSRLSNLIKLAQKVPTADLEDVLPLAEDITNILSKCCESASEDCMAKELPEHTVKLCDNLSTKNSKFEDCCQEKTAMDVFVCTYFMPAAQLP
4	P02774-D4	322-399	78		ELPDVELPTNKDVCDPGNTKVMDKYTFELSRRTHLPEVFLSKVLEPTLKSLGECCDVEDSTTCFNAKGPLLKKELSSF
5	P02774-D5	400-474	75		IDKGQELCADYSENTFTEYKKKLAERLKAKLPDATPTELAKLVNKHSDFASNCCSINSPPLYCDSEIDAELKNIL

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.928

(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	1kw2A	0.95	0.84	0.996	0.960	model1_1kw2A.pdb.gz
2	7yimA	0.51	6.27	0.100	0.768	model1_7yimA.pdb.gz
3	5oklA	0.49	5.48	0.140	0.643	model1_5oklA.pdb.gz
4	1n5uA	0.47	5.75	0.105	0.639	model1_1n5uA.pdb.gz
5	6vr4A	0.44	7.26	0.037	0.713	model1_6vr4A.pdb.gz
6	7vk9A	0.43	7.20	0.053	0.694	model1_7vk9A.pdb.gz
7	4cmpA	0.41	7.39	0.065	0.686	model1_4cmpA.pdb.gz
8	6w2jA	0.40	7.18	0.033	0.654	model1_6w2jA.pdb.gz
9	6xjaP	0.40	7.24	0.064	0.654	model1_6xjaP.pdb.gz
10	6v85A	0.40	7.43	0.037	0.667	model1_6v85A.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:0097159	0.86	organic cyclic compound binding
GO:0008289	0.76	lipid binding
GO:1901363	0.55	heterocyclic compound binding
GO:0036094	0.55	small molecule binding
GO:0043167	0.52	ion 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:0044699	1.00	single-organism process
GO:1902578	0.83	single-organism localization
GO:0065007	0.74	biological regulation
GO:0050896	0.66	response to stimulus
GO:0065008	0.65	regulation of biological quality
GO:0050789	0.65	regulation of biological process
GO:0051704	0.63	multi-organism process
GO:0009987	0.62	cellular process
GO:0009605	0.59	response to external stimulus
GO:0050794	0.58	regulation of cellular process
GO:0031667	0.58	response to nutrient levels
GO:0044763	0.57	single-organism cellular process
GO:0008152	0.55	metabolic process
GO:0048519	0.52	negative regulation of biological process
GO:0048523	0.50	negative regulation of cellular process

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	0.78	cell part
GO:0044424	0.73	intracellular part
GO:0044421	0.67	extracellular region part
GO:0005615	0.63	extracellular space
GO:0044444	0.60	cytoplasmic part
GO:0043226	0.56	organelle
GO:0043227	0.55	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	1dmtA	0.352	7.22	0.028	0.578	3.4.24.11	NA
2	0.060	1mdwA	0.216	6.45	0.088	0.325	3.4.22.53	NA
3	0.060	1ofdA	0.378	7.47	0.048	0.637	1.4.7.1	NA
4	0.060	1r1jA	0.354	7.33	0.040	0.595	3.4.24.11	209,217
5	0.060	5r1rA	0.343	7.57	0.065	0.574	1.17.4.1	266

	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	0.02	2ydfA	0.508	6.54	0.111	0.778	0.24	IO3	complex1.pdb.gz	163,220,221
2	0.01	2vueB	0.500	6.63	0.125	0.785	0.30	BLA	complex2.pdb.gz	182,210,213,214
3	0.01	2vufB	0.507	6.58	0.116	0.776	0.24	FUA	complex3.pdb.gz	221,224,225
4	0.01	2xvvA	0.483	5.69	0.116	0.652	0.30	9DN	complex4.pdb.gz	220,223,224
5	0.01	2bxiA	0.471	5.48	0.135	0.633	0.23	AZQ	complex5.pdb.gz	215,218,219,222,223
6	0.01	2xw0A	0.506	6.53	0.111	0.774	0.16	9NF	complex6.pdb.gz	57,60,61,63
7	0.01	2bxgA	0.515	6.59	0.108	0.791	0.10	IBP	complex7.pdb.gz	106,107,227

	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.