D-I-TASSER O00483

D-I-TASSER results for O00483

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

Summary of the Protein

Uniprot ID: O00483
Protein Name: Cytochrome c oxidase subunit NDUFA4
Gene Name: NDUFA4

Input Sequence in FASTA format

>O00483 (81 residues)
MLRQIIGQAKKHPSLIPLFVFIGTGATGATLYLLRLALFNPDVCWDRNNPEPWNKLGPND
QYKFYSVNVDYSKLKKERPDF

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	O00483-D1	1-81	81		MLRQIIGQAKKHPSLIPLFVFIGTGATGATLYLLRLALFNPDVCWDRNNPEPWNKLGPNDQYKFYSVNVDYSKLKKERPDF

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.7876

(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	5z62N	0.72	1.99	0.584	0.951	model1_5z62N.pdb.gz
2	7taoA	0.58	3.49	0.013	0.876	model1_7taoA.pdb.gz
3	6o7ua	0.58	3.59	0.053	0.876	model1_6o7ua.pdb.gz
4	7qe7N	0.58	3.23	0.065	0.914	model1_7qe7N.pdb.gz
5	7m75A	0.57	3.21	0.096	0.852	model1_7m75A.pdb.gz
6	6qd6A1	0.57	3.38	0.056	0.827	model1_6qd6A1.pdb.gz
7	5ez3A	0.57	3.66	0.039	0.864	model1_5ez3A.pdb.gz
8	8a3tQ	0.56	3.84	0.093	0.901	model1_8a3tQ.pdb.gz
9	6xv8B	0.56	3.29	0.056	0.827	model1_6xv8B.pdb.gz
10	6m9tA2	0.56	3.17	0.095	0.815	model1_6m9tA2.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:0004129	1.00	cytochrome-c oxidase activity
GO:0016651	0.95	oxidoreductase activity, acting on NAD(P)H
GO:0008137	0.94	NADH dehydrogenase (ubiquinone) 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:0006123	1.00	mitochondrial electron transport, cytochrome c to oxygen
GO:0006120	1.00	mitochondrial electron transport, NADH to ubiquinone

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:0005751	1.00	mitochondrial respiratory chain complex IV

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	3cf4A	0.504	3.64	0.064	0.815	1.2.99.2	NA
2	0.060	3d3lA	0.527	3.70	0.108	0.864	1.13.11.31	NA
3	0.060	2zr3B	0.466	3.31	0.055	0.704	6.1.1.11	NA
4	0.060	2z1qB	0.513	3.76	0.038	0.840	1.3.99.3	NA
5	0.060	2fonB	0.453	3.84	0.027	0.753	1.3.3.6	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	0.02	2gdcA	0.576	3.53	0.096	0.876	0.29	III	complex1.pdb.gz	19,26,30,33,34,38
2	0.01	3d36A	0.556	3.60	0.105	0.938	0.22	ADP	complex2.pdb.gz	30,32,33,34,35
3	0.01	2gwwA	0.549	3.42	0.096	0.864	0.27	III	complex3.pdb.gz	22,25,26,29,32,33,36,40
4	0.01	1t01A	0.546	3.31	0.085	0.840	0.26	III	complex4.pdb.gz	20,24,27,31,34,35
5	0.01	1xwjA	0.553	3.83	0.092	0.889	0.22	III	complex5.pdb.gz	19,22,23,26,27,30,33
6	0.01	1mo8A	0.260	3.33	0.121	0.370	0.21	ATP	complex6.pdb.gz	22,24,25,26
7	0.01	1zvzA	0.502	3.73	0.026	0.815	0.23	III	complex7.pdb.gz	24,27,28,31,34,35,64
8	0.01	2dq3A	0.551	3.53	0.027	0.840	0.10	SSA	complex8.pdb.gz	25,26,29,34
9	0.01	2hsqA	0.508	3.26	0.000	0.790	0.23	III	complex9.pdb.gz	1,2,13,19,20,26,27,30,33
10	0.01	3u33J	0.548	3.73	0.066	0.889	0.10	FAD	complex10.pdb.gz	27,29,30,33

	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.