D-I-TASSER Q16654

D-I-TASSER results for Q16654

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

Summary of the Protein

Uniprot ID: Q16654
Protein Name: [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 4, mitochondrial
Gene Name: PDK4

Input Sequence in FASTA format

>Q16654 (411 residues)
MKAARFVLRSAGSLNGAGLVPREVEHFSRYSPSPLSMKQLLDFGSENACERTSFAFLRQE
LPVRLANILKEIDILPTQLVNTSSVQLVKSWYIQSLMDLVEFHEKSPDDQKALSDFVDTL
IKVRNRHHNVVPTMAQGIIEYKDACTVDPVTNQNLQYFLDRFYMNRISTRMLMNQHILIF
SDSQTGNPSHIGSIDPNCDVVAVVQDAFECSRMLCDQYYLSSPELKLTQVNGKFPDQPIH
IVYVPSHLHHMLFELFKNAMRATVEHQENQPSLTPIEVIVVLGKEDLTIKISDRGGGVPL
RIIDRLFSYTYSTAPTPVMDNSRNAPLAGFGYGLPISRLYAKYFQGDLNLYSLSGYGTDA
IIYLKALSSESIEKLPVFNKSAFKHYQMSSEADDWCIPSREPKNLAKEVAM

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	Q16654-D1	1-188	188		MKAARFVLRSAGSLNGAGLVPREVEHFSRYSPSPLSMKQLLDFGSENACERTSFAFLRQELPVRLANILKEIDILPTQLVNTSSVQLVKSWYIQSLMDLVEFHEKSPDDQKALSDFVDTLIKVRNRHHNVVPTMAQGIIEYKDACTVDPVTNQNLQYFLDRFYMNRISTRMLMNQHILIFSDSQTGNP
2	Q16654-D2	189-411	223		SHIGSIDPNCDVVAVVQDAFECSRMLCDQYYLSSPELKLTQVNGKFPDQPIHIVYVPSHLHHMLFELFKNAMRATVEHQENQPSLTPIEVIVVLGKEDLTIKISDRGGGVPLRIIDRLFSYTYSTAPTPVMDNSRNAPLAGFGYGLPISRLYAKYFQGDLNLYSLSGYGTDAIIYLKALSSESIEKLPVFNKSAFKHYQMSSEADDWCIPSREPKNLAKEVAM

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.785

(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	3crlB	0.87	1.97	0.634	0.905	model1_3crlB.pdb.gz
2	1y8pA	0.86	1.83	0.636	0.905	model1_1y8pA.pdb.gz
3	3d2rB	0.85	1.45	1.000	0.881	model1_3d2rB.pdb.gz
4	2q8gA	0.84	2.16	0.651	0.893	model1_2q8gA.pdb.gz
5	1gkzA	0.71	2.31	0.304	0.757	model1_1gkzA.pdb.gz
6	3dgeA	0.38	3.05	0.127	0.428	model1_3dgeA.pdb.gz
7	3d36B	0.36	3.23	0.152	0.406	model1_3d36B.pdb.gz
8	4gczA2	0.34	2.78	0.150	0.370	model1_4gczA2.pdb.gz
9	3sl2A	0.32	2.34	0.189	0.345	model1_3sl2A.pdb.gz
10	4cl4A	0.30	6.50	0.053	0.470	model1_4cl4A.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	0.97	catalytic activity
GO:0016740	0.96	transferase activity
GO:0016301	0.95	kinase activity
GO:0004672	0.93	protein kinase activity
GO:0004740	0.79	pyruvate dehydrogenase (acetyl-transferring) kinase activity
GO:1901363	0.71	heterocyclic compound binding
GO:0097159	0.71	organic cyclic compound binding
GO:0097367	0.70	carbohydrate derivative binding
GO:0000166	0.70	nucleotide binding
GO:0005524	0.69	ATP 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:0009987	0.96	cellular process
GO:0044699	0.93	single-organism process
GO:0065007	0.89	biological regulation
GO:0008152	0.87	metabolic process
GO:0044763	0.85	single-organism cellular process
GO:0050789	0.81	regulation of biological process
GO:0050794	0.80	regulation of cellular process
GO:0044237	0.76	cellular metabolic process
GO:0007165	0.75	signal transduction
GO:0080090	0.73	regulation of primary metabolic process
GO:0031323	0.73	regulation of cellular metabolic process
GO:0010906	0.70	regulation of glucose metabolic process
GO:0009889	0.68	regulation of biosynthetic process
GO:0031326	0.67	regulation of cellular biosynthetic process
GO:0050896	0.66	response to stimulus
GO:0010510	0.66	regulation of acetyl-CoA biosynthetic process from pyruvate
GO:0071704	0.64	organic substance metabolic process
GO:0051716	0.64	cellular response to stimulus
GO:0042221	0.64	response to chemical
GO:0070887	0.63	cellular response to chemical stimulus
GO:1901701	0.56	cellular response to oxygen-containing compound
GO:0044238	0.55	primary metabolic process
GO:0007166	0.54	cell surface receptor signaling pathway
GO:0065008	0.50	regulation of biological quality

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	0.99	cytoplasmic part
GO:0043226	0.91	organelle
GO:0043231	0.90	intracellular membrane-bounded organelle
GO:0005739	0.88	mitochondrion
GO:0044446	0.75	intracellular organelle part
GO:0044429	0.66	mitochondrial part

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	0.667	2zdxA	0.796	1.29	0.997	0.820	2.7.11.2	250,254
2	0.654	1y8pA	0.864	1.83	0.636	0.905	2.7.11.2	250,254
3	0.590	3crlB	0.866	1.97	0.634	0.905	2.7.11.2	250,253,257,261,303,306,308,312,328,330,332,334,336,338,340,350
4	0.400	1gkzA	0.711	2.31	0.304	0.757	2.7.11.4 2.7.1.115	254
5	0.281	3d2rB	0.852	1.45	1.000	0.881	2.7.11.2	250,254

	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:

Click to view	Rank	Cscore^LB	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	BS-score	Lig. Name	Download Complex	Predicted binding site residues
	1	0.36	2btz0	0.827	1.87	0.664	0.869	1.61	III	complex1.pdb.gz	32,157,161,164,230,232,279,283,284,285,286,288,290,299,300,301,351,352,353,354,355,356,359,363,374,375,376,377,379,381,382,395
	2	0.11	2bu7A	0.832	1.82	0.662	0.871	1.17	TF3	complex2.pdb.gz	75,76,78,79,85,134,137,138,141,159

	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.