D-I-TASSER P39656

D-I-TASSER results for P39656

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

Summary of the Protein

Uniprot ID: P39656
Protein Name: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kDa subunit
Gene Name: DDOST

Input Sequence in FASTA format

>P39656 (456 residues)
MGYFRCARAGSFGRRRKMEPSTAARAWALFWLLLPLLGAVCASGPRTLVLLDNLNVRETH
SLFFRSLKDRGFELTFKTADDPSLSLIKYGEFLYDNLIIFSPSVEDFGGNINVETISAFI
DGGGSVLVAASSDIGDPLRELGSECGIEFDEEKTAVIDHHNYDISDLGQHTLIVADTENL
LKAPTIVGKSSLNPILFRGVGMVADPDNPLVLDILTGSSTSYSFFPDKPITQYPHAVGKN
TLLIAGLQARNNARVIFSGSLDFFSDSFFNSAVQKAAPGSQRYSQTGNYELAVALSRWVF
KEEGVLRVGPVSHHRVGETAPPNAYTVTDLVEYSIVIQQLSNGKWVPFDGDDIQLEFVRI
DPFVRTFLKKKGGKYSVQFKLPDVYGVFQFKVDYNRLGYTHLYSSTQVSVRPLQHTQYER
FIPSAYPYYASAFSMMLGLFIFSIVFLHMKEKEKSD

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	P39656-D1	1-302	302		MGYFRCARAGSFGRRRKMEPSTAARAWALFWLLLPLLGAVCASGPRTLVLLDNLNVRETHSLFFRSLKDRGFELTFKTADDPSLSLIKYGEFLYDNLIIFSPSVEDFGGNINVETISAFIDGGGSVLVAASSDIGDPLRELGSECGIEFDEEKTAVIDHHNYDISDLGQHTLIVADTENLLKAPTIVGKSSLNPILFRGVGMVADPDNPLVLDILTGSSTSYSFFPDKPITQYPHAVGKNTLLIAGLQARNNARVIFSGSLDFFSDSFFNSAVQKAAPGSQRYSQTGNYELAVALSRWVFKE
2	P39656-D2	303-456	154		EGVLRVGPVSHHRVGETAPPNAYTVTDLVEYSIVIQQLSNGKWVPFDGDDIQLEFVRIDPFVRTFLKKKGGKYSVQFKLPDVYGVFQFKVDYNRLGYTHLYSSTQVSVRPLQHTQYERFIPSAYPYYASAFSMMLGLFIFSIVFLHMKEKEKSD

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.84

(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	6s7oG	0.90	0.61	1.000	0.901	model1_6s7oG.pdb.gz
2	6eznG	0.79	2.01	0.253	0.833	model1_6eznG.pdb.gz
3	8bd7B	0.43	3.52	0.111	0.502	model1_8bd7B.pdb.gz
4	7zu9A	0.43	5.20	0.060	0.566	model1_7zu9A.pdb.gz
5	6lvbA2	0.41	4.65	0.086	0.520	model1_6lvbA2.pdb.gz
6	4jqsA	0.41	3.97	0.150	0.487	model1_4jqsA.pdb.gz
7	6nwzA	0.40	4.53	0.074	0.504	model1_6nwzA.pdb.gz
8	8huyA	0.40	4.58	0.085	0.504	model1_8huyA.pdb.gz
9	7w8jA	0.40	4.77	0.083	0.513	model1_7w8jA.pdb.gz
10	4e5vA	0.40	4.09	0.120	0.482	model1_4e5vA.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:0003824	0.99	catalytic activity
GO:0004576	0.98	oligosaccharyl transferase 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:0009987	0.99	cellular process
GO:0044763	0.98	single-organism cellular process
GO:0071704	0.97	organic substance metabolic process
GO:0044237	0.97	cellular metabolic process
GO:0044260	0.96	cellular macromolecule metabolic process
GO:0044238	0.96	primary metabolic process
GO:0044267	0.95	cellular protein metabolic process
GO:0044710	0.94	single-organism metabolic process
GO:0006464	0.94	cellular protein modification process
GO:0006486	0.93	protein glycosylation

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:0044424	1.00	intracellular part
GO:0044444	0.98	cytoplasmic part
GO:0044446	0.95	intracellular organelle part
GO:0044432	0.94	endoplasmic reticulum part
GO:0044425	0.94	membrane part
GO:0032991	0.94	macromolecular complex
GO:0098796	0.93	membrane protein complex
GO:0008250	0.92	oligosaccharyltransferase 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	2ckjA	0.324	7.05	0.042	0.528	1.17.1.4 1.17.3.2	NA
2	0.060	1qhaA	0.364	7.23	0.037	0.592	2.7.1.1	NA
3	0.060	1vcoA	0.377	5.10	0.051	0.489	6.3.4.2	NA
4	0.060	3kvnX	0.366	6.75	0.046	0.570	3.1.1.1	291
5	0.060	1cvrA	0.374	5.81	0.061	0.546	3.4.22.37	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	0.01	2h2w0	0.384	4.02	0.103	0.467	0.31	III	complex1.pdb.gz	71,72,187,188,189,273,286,287,288,289,292,293,300,301
2	0.01	1dgkN	0.369	7.50	0.045	0.625	0.18	GLC	complex2.pdb.gz	90,91,112,120
3	0.01	2nztB	0.385	7.27	0.041	0.638	0.19	GLC	complex3.pdb.gz	91,92,93,111,116
4	0.01	3ottB	0.382	6.43	0.033	0.566	0.24	TBR	complex4.pdb.gz	90,91,118
5	0.01	1bg3B	0.362	7.10	0.048	0.590	0.23	G6P	complex5.pdb.gz	85,95,120
6	0.01	2q3zA	0.369	6.64	0.051	0.566	0.11	III	complex6.pdb.gz	41,46,91,92
7	0.01	2zuuA	0.370	4.73	0.096	0.471	0.13	NDG	complex7.pdb.gz	42,94,95
8	0.01	2zutA	0.370	4.68	0.097	0.469	0.11	A2G	complex8.pdb.gz	244,245,246
9	0.01	1qhaA	0.364	7.23	0.037	0.592	0.18	GLC	complex9.pdb.gz	124,125,126,299
10	0.01	2ad5B	0.365	4.83	0.042	0.469	0.12	ADP	complex10.pdb.gz	259,260,261

	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.