D-I-TASSER O76003

D-I-TASSER results for O76003

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

Summary of the Protein

Uniprot ID: O76003
Protein Name: Glutaredoxin-3
Gene Name: GLRX3

Input Sequence in FASTA format

>O76003 (335 residues)
MAAGAAEAAVAAVEEVGSAGQFEELLRLKAKSLLVVHFWAPWAPQCAQMNEVMAELAKEL
PQVSFVKLEAEGVPEVSEKYEISSVPTFLFFKNSQKIDRLDGAHAPELTKKVQRHASSGS
FLPSANEHLKEDLNLRLKKLTHAAPCMLFMKGTPQEPRCGFSKQMVEILHKHNIQFSSFD
IFSDEEVRQGLKAYSSWPTYPQLYVSGELIGGLDIIKELEASEELDTICPKAPKLEERLK
VLTNKASVMLFMKGNKQEAKCGFSKQILEILNSTGVEYETFDILEDEEVRQGLKAYSNWP
TYPQLYVKGELVGGLDIVKELKENGELLPILRGEN

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	O76003-D1	1-118	118		MAAGAAEAAVAAVEEVGSAGQFEELLRLKAKSLLVVHFWAPWAPQCAQMNEVMAELAKELPQVSFVKLEAEGVPEVSEKYEISSVPTFLFFKNSQKIDRLDGAHAPELTKKVQRHASS
2	O76003-D2	119-233	115		GSFLPSANEHLKEDLNLRLKKLTHAAPCMLFMKGTPQEPRCGFSKQMVEILHKHNIQFSSFDIFSDEEVRQGLKAYSSWPTYPQLYVSGELIGGLDIIKELEASEELDTICPKAP
3	O76003-D3	234-335	102		KLEERLKVLTNKASVMLFMKGNKQEAKCGFSKQILEILNSTGVEYETFDILEDEEVRQGLKAYSNWPTYPQLYVKGELVGGLDIVKELKENGELLPILRGEN

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.72

(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	5xf7A	0.43	5.97	0.090	0.645	model1_5xf7A.pdb.gz
2	3sggA	0.40	6.12	0.054	0.624	model1_3sggA.pdb.gz
3	2c4mC	0.40	6.52	0.082	0.660	model1_2c4mC.pdb.gz
4	5lr8A	0.40	6.37	0.087	0.642	model1_5lr8A.pdb.gz
5	4l22A	0.40	6.32	0.077	0.639	model1_4l22A.pdb.gz
6	4bqeA	0.40	6.32	0.094	0.639	model1_4bqeA.pdb.gz
7	2aw3A	0.39	6.31	0.086	0.630	model1_2aw3A.pdb.gz
8	6y55A	0.39	6.05	0.035	0.606	model1_6y55A.pdb.gz
9	1ygpA	0.39	6.58	0.061	0.645	model1_1ygpA.pdb.gz
10	2r8oB	0.38	6.46	0.052	0.630	model1_2r8oB.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	0.96	catalytic activity
GO:0016491	0.78	oxidoreductase activity
GO:0016667	0.73	oxidoreductase activity, acting on a sulfur group of donors
GO:0015036	0.72	disulfide oxidoreductase activity
GO:0015035	0.69	protein disulfide oxidoreductase activity
GO:0016671	0.67	oxidoreductase activity, acting on a sulfur group of donors, disulfide as acceptor

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	0.96	cellular process
GO:0044699	0.86	single-organism process
GO:0065007	0.82	biological regulation
GO:0008152	0.82	metabolic process
GO:0050896	0.81	response to stimulus
GO:0050789	0.80	regulation of biological process
GO:0006950	0.79	response to stress
GO:0044237	0.78	cellular metabolic process
GO:0033554	0.77	cellular response to stress
GO:0044763	0.76	single-organism cellular process
GO:0006457	0.75	protein folding
GO:0050794	0.74	regulation of cellular process
GO:0065008	0.72	regulation of biological quality
GO:0044710	0.72	single-organism metabolic process
GO:0042592	0.67	homeostatic process
GO:0019725	0.65	cellular homeostasis
GO:0045454	0.64	cell redox homeostasis
GO:0042221	0.64	response to chemical
GO:0006979	0.63	response to oxidative stress
GO:0006790	0.63	sulfur compound metabolic process
GO:0034599	0.62	cellular response to oxidative stress
GO:0055114	0.61	oxidation-reduction process
GO:0000103	0.61	sulfate assimilation

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	1.00	cell part
GO:0044424	0.99	intracellular part
GO:0044444	0.82	cytoplasmic part
GO:0043226	0.64	organelle
GO:0043227	0.62	membrane-bounded organelle
GO:0043229	0.58	intracellular organelle
GO:0043231	0.57	intracellular 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	3f41A	0.364	6.82	0.030	0.630	3.1.3.8	NA
2	0.060	1gpmA	0.381	6.87	0.065	0.672	6.3.5.2	NA
3	0.060	2vxoB	0.381	7.01	0.070	0.678	6.3.5.2	NA
4	0.060	1xc6A	0.364	6.63	0.053	0.612	3.2.1.23	NA
5	0.060	1fa9A	0.396	6.27	0.054	0.636	2.4.1.1	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	0.01	3e3nF	0.392	6.22	0.054	0.627	0.41	AMP	complex1.pdb.gz	239,243,309,311
2	0.01	2iegA	0.387	6.10	0.039	0.609	0.43	FRY	complex2.pdb.gz	152,161,165,303
3	0.01	2ieiA	0.387	6.09	0.039	0.606	0.42	FRX	complex3.pdb.gz	150,152,161,165,267
4	0.01	2iegB	0.388	6.08	0.053	0.609	0.42	FRY	complex4.pdb.gz	149,150,187,191
5	0.01	1gfzA	0.389	6.15	0.035	0.612	0.46	CFF	complex5.pdb.gz	303,314,315
6	0.01	1l7xB	0.394	6.19	0.049	0.627	0.46	700	complex6.pdb.gz	153,161,165,303
7	0.01	1l7xA	0.394	6.10	0.043	0.615	0.51	700	complex7.pdb.gz	161,264,302,303
8	0.01	1xoiB	0.393	6.14	0.046	0.624	0.46	288	complex8.pdb.gz	153,161,165,301,302,303
9	0.01	2zb2A	0.392	6.02	0.035	0.609	0.56	A46	complex9.pdb.gz	149,150,151,289,293

	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.