D-I-TASSER P03897

D-I-TASSER results for P03897

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

Summary of the Protein

Uniprot ID: P03897
Protein Name: NADH-ubiquinone oxidoreductase chain 3
Gene Name: MT-ND3

Input Sequence in FASTA format

>P03897 (115 residues)
MNFALILMINTLLALLLMIITFWLPQLNGYMEKSTPYECGFDPMSPARVPFSMKFFLVAI
TFLLFDLEIALLLPLPWALQTTNLPLMVMSSLLLIIILALSLAYEWLQKGLDWTE

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	P03897-D1	1-115	115		MNFALILMINTLLALLLMIITFWLPQLNGYMEKSTPYECGFDPMSPARVPFSMKFFLVAITFLLFDLEIALLLPLPWALQTTNLPLMVMSSLLLIIILALSLAYEWLQKGLDWTE

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.6228

(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	6ek7A	0.62	3.22	0.069	0.844	model1_6ek7A.pdb.gz
2	6gbhC	0.62	3.93	0.124	0.939	model1_6gbhC.pdb.gz
3	6u4oC	0.62	2.85	0.074	0.826	model1_6u4oC.pdb.gz
4	1jswB	0.61	2.97	0.095	0.826	model1_1jswB.pdb.gz
5	1m56A1	0.61	3.40	0.063	0.878	model1_1m56A1.pdb.gz
6	4zh0A1	0.61	3.97	0.080	0.913	model1_4zh0A1.pdb.gz
7	6iiuA	0.61	3.76	0.053	0.930	model1_6iiuA.pdb.gz
8	6hwhZ	0.61	3.05	0.031	0.852	model1_6hwhZ.pdb.gz
9	4gzuA1	0.61	2.96	0.103	0.844	model1_4gzuA1.pdb.gz
10	6t15a1	0.61	3.09	0.070	0.835	model1_6t15a1.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:0016491	1.00	oxidoreductase activity
GO:0016655	0.95	oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor
GO:0050136	0.90	NADH dehydrogenase (quinone) activity
GO:0008137	0.67	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:0009987	0.91	cellular process
GO:0044699	0.87	single-organism process
GO:0008152	0.87	metabolic process
GO:0044710	0.82	single-organism metabolic process
GO:0044237	0.73	cellular metabolic process
GO:0044763	0.71	single-organism cellular process
GO:0055114	0.65	oxidation-reduction process
GO:0006091	0.65	generation of precursor metabolites and energy
GO:0022904	0.64	respiratory electron transport chain
GO:0006120	0.62	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:0044464	1.00	cell part
GO:0044424	0.99	intracellular part
GO:0044444	0.98	cytoplasmic part
GO:0044446	0.69	intracellular organelle part
GO:0044429	0.65	mitochondrial part
GO:0043226	0.65	organelle
GO:0043229	0.64	intracellular organelle
GO:0043227	0.63	membrane-bounded organelle
GO:0043231	0.62	intracellular membrane-bounded organelle
GO:0044425	0.60	membrane part
GO:0032991	0.58	macromolecular complex
GO:0043234	0.57	protein complex
GO:1902494	0.56	catalytic complex
GO:0098796	0.56	membrane protein complex
GO:1990204	0.55	oxidoreductase complex
GO:0098803	0.55	respiratory chain complex
GO:0045271	0.54	respiratory chain complex I
GO:0044455	0.52	mitochondrial membrane part
GO:0098800	0.51	inner mitochondrial membrane protein 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	2ix6A	0.577	3.97	0.045	0.904	1.3.3.6	NA
2	0.060	1dofA	0.576	3.03	0.129	0.809	4.3.2.2	NA
3	0.060	2ix6E	0.578	3.98	0.054	0.904	1.3.3.6	NA
4	0.060	1qleC	0.559	3.36	0.043	0.817	1.9.3.1	60,103
5	0.060	1occA	0.582	3.15	0.112	0.817	1.9.3.1	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	0.04	1ocoN	0.587	3.13	0.122	0.817	0.17	HEA	complex1.pdb.gz	54,61,63,64,68,72
2	0.03	1ocoA	0.587	3.13	0.122	0.817	0.13	HEA	complex2.pdb.gz	53,59,63,67,71,74
3	0.03	2eijN	0.588	3.08	0.112	0.817	0.20	HEA	complex3.pdb.gz	39,40,62,63,65,66,72,95,99,102
4	0.01	3swoA	0.594	3.99	0.072	0.922	0.34	FDA	complex4.pdb.gz	37,41,110,111
5	0.01	3eh5A	0.584	3.24	0.085	0.852	0.14	HEM	complex5.pdb.gz	14,17,18,20,21
6	0.01	2jbsA	0.552	4.48	0.035	0.904	0.20	FMN	complex6.pdb.gz	13,17,40,41,42,55,56

	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.