D-I-TASSER O14521

D-I-TASSER results for O14521

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

Summary of the Protein

Uniprot ID: O14521
Protein Name: Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial
Gene Name: SDHD

Input Sequence in FASTA format

>O14521 (159 residues)
MAVLWRLSAVCGALGGRALLLRTPVVRPAHISAFLQDRPIPEWCGVQHIHLSPSHHSGSK
AASLHWTSERVVSVLLLGLLPAAYLNPCSAMDYSLAAALTLHGHWGLGQVVTDYVHGDAL
QKAAKAGLLALSALTFAGLCYFNYHDVGICKAVAMLWKL

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	O14521-D1	1-159	159		MAVLWRLSAVCGALGGRALLLRTPVVRPAHISAFLQDRPIPEWCGVQHIHLSPSHHSGSKAASLHWTSERVVSVLLLGLLPAAYLNPCSAMDYSLAAALTLHGHWGLGQVVTDYVHGDALQKAAKAGLLALSALTFAGLCYFNYHDVGICKAVAMLWKL

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.6594

(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	1zp0D	0.60	1.58	0.951	0.641	model1_1zp0D.pdb.gz
2	5v6pA2	0.58	3.81	0.067	0.761	model1_5v6pA2.pdb.gz
3	3vr8D	0.56	2.03	0.336	0.641	model1_3vr8D.pdb.gz
4	6lo8D	0.56	2.13	0.182	0.635	model1_6lo8D.pdb.gz
5	2ncjA	0.55	3.89	0.055	0.792	model1_2ncjA.pdb.gz
6	5twvB	0.55	3.87	0.082	0.780	model1_5twvB.pdb.gz
7	5b2nA	0.54	4.01	0.071	0.748	model1_5b2nA.pdb.gz
8	7jh5A	0.54	4.20	0.077	0.811	model1_7jh5A.pdb.gz
9	6uo8A	0.53	3.88	0.038	0.748	model1_6uo8A.pdb.gz
10	6nwfA	0.53	4.26	0.110	0.774	model1_6nwfA.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	0.89	catalytic activity
GO:0016491	0.87	oxidoreductase activity
GO:0000104	0.84	succinate dehydrogenase activity
GO:1901363	0.61	heterocyclic compound binding
GO:0097159	0.61	organic cyclic compound binding
GO:0048037	0.55	cofactor binding
GO:0048039	0.54	ubiquinone binding
GO:0020037	0.54	heme 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:0006099	1.00	tricarboxylic acid cycle

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:0044429	1.00	mitochondrial part
GO:0005740	0.75	mitochondrial envelope
GO:0044425	0.65	membrane part
GO:0032991	0.63	macromolecular complex
GO:0016020	0.63	membrane
GO:0043234	0.62	protein complex
GO:0044455	0.61	mitochondrial membrane part
GO:1902494	0.60	catalytic complex
GO:0098800	0.60	inner mitochondrial membrane protein complex
GO:0031090	0.60	organelle membrane
GO:1990204	0.59	oxidoreductase complex
GO:0098803	0.59	respiratory chain complex
GO:0031966	0.59	mitochondrial membrane
GO:0005743	0.58	mitochondrial inner membrane
GO:0005749	0.55	mitochondrial respiratory chain complex II, succinate dehydrogenase complex (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 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	0.600	2h89D	0.604	1.50	0.784	0.641	1.3.5.1	66,68,72,75,77,95,97,99,101,103,105,108,110,136
2	0.060	1iduA	0.474	4.19	0.070	0.717	1.11.1.10	NA
3	0.060	2a06C	0.485	4.53	0.096	0.742	1.10.2.2	NA
4	0.060	3lomA	0.476	4.78	0.085	0.799	2.5.1.10	NA
5	0.060	3ffzA	0.463	4.96	0.047	0.748	3.4.24.69	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	0.71	3ae4D	0.601	1.61	0.951	0.641	1.97	HEM	complex1.pdb.gz	70,76,77,80,102,106,107
2	0.45	3aefD	0.603	1.61	0.951	0.641	1.96	EPH	complex2.pdb.gz	80,83,84,87,99,153,154,157
3	0.38	2h88D	0.604	1.31	0.792	0.635	1.76	UNL	complex3.pdb.gz	100,103,104,107,131,132,135
4	0.02	3abwD	0.520	4.38	0.126	0.774	0.84	AZI	complex4.pdb.gz	97,100,135,136,139
5	0.02	3a7kD	0.524	4.58	0.125	0.780	0.82	22B	complex5.pdb.gz	68,72,97,101,105,109

	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.