D-I-TASSER P54819

D-I-TASSER results for P54819

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

Summary of the Protein

Uniprot ID: P54819
Protein Name: Adenylate kinase 2, mitochondrial
Gene Name: AK2

Input Sequence in FASTA format

>P54819 (239 residues)
MAPSVPAAEPEYPKGIRAVLLGPPGAGKGTQAPRLAENFCVCHLATGDMLRAMVASGSEL
GKKLKATMDAGKLVSDEMVVELIEKNLETPLCKNGFLLDGFPRTVRQAEMLDDLMEKRKE
KLDSVIEFSIPDSLLIRRITGRLIHPKSGRSYHEEFNPPKEPMKDDITGEPLIRRSDDNE
KALKIRLQAYHTQTTPLIEYYRKRGIHSAIDASQTPDVVFASILAAFSKATCKDLVMFI

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	P54819-D1	1-129,206-239	163		MAPSVPAAEPEYPKGIRAVLLGPPGAGKGTQAPRLAENFCVCHLATGDMLRAMVASGSELGKKLKATMDAGKLVSDEMVVELIEKNLETPLCKNGFLLDGFPRTVRQAEMLDDLMEKRKEKLDSVIEFSIHSAIDASQTPDVVFASILAAFSKATCKDLVMFI
2	P54819-D2	130-205	76		IPDSLLIRRITGRLIHPKSGRSYHEEFNPPKEPMKDDITGEPLIRRSDDNEKALKIRLQAYHTQTTPLIEYYRKRG

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.854

(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	3tlxA	0.88	1.53	0.454	0.925	model1_3tlxA.pdb.gz
2	3akyA	0.86	1.51	0.576	0.908	model1_3akyA.pdb.gz
3	3be4A	0.85	1.62	0.437	0.900	model1_3be4A.pdb.gz
4	3dl0A	0.84	1.71	0.389	0.904	model1_3dl0A.pdb.gz
5	5g3yA	0.84	1.50	0.493	0.891	model1_5g3yA.pdb.gz
6	1zakA	0.82	2.18	0.359	0.904	model1_1zakA.pdb.gz
7	3hprA	0.81	1.69	0.488	0.875	model1_3hprA.pdb.gz
8	2rgxA	0.80	1.52	0.463	0.849	model1_2rgxA.pdb.gz
9	2cdnA	0.73	1.67	0.414	0.774	model1_2cdnA.pdb.gz
10	1qf9A	0.72	2.10	0.278	0.791	model1_1qf9A.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	0.95	catalytic activity
GO:0019205	0.94	nucleobase-containing compound kinase activity
GO:0016776	0.93	phosphotransferase activity, phosphate group as acceptor
GO:0019201	0.70	nucleotide kinase activity
GO:0004017	0.62	adenylate kinase 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	0.96	cellular process
GO:0044699	0.95	single-organism process
GO:0044763	0.92	single-organism cellular process
GO:0008152	0.92	metabolic process
GO:0071704	0.89	organic substance metabolic process
GO:0044237	0.89	cellular metabolic process
GO:0044238	0.88	primary metabolic process
GO:0006807	0.87	nitrogen compound metabolic process
GO:0034641	0.86	cellular nitrogen compound metabolic process
GO:0044281	0.84	small molecule metabolic process
GO:0006139	0.82	nucleobase-containing compound metabolic process
GO:0055086	0.80	nucleobase-containing small molecule metabolic process
GO:1901576	0.71	organic substance biosynthetic process
GO:0044249	0.71	cellular biosynthetic process
GO:0044271	0.69	cellular nitrogen compound biosynthetic process
GO:0044711	0.64	single-organism biosynthetic process
GO:0006753	0.64	nucleoside phosphate metabolic process
GO:1901362	0.63	organic cyclic compound biosynthetic process
GO:0018130	0.63	heterocycle biosynthetic process
GO:0009117	0.63	nucleotide metabolic process
GO:0034654	0.58	nucleobase-containing compound biosynthetic process
GO:1901564	0.55	organonitrogen compound metabolic process
GO:1901293	0.55	nucleoside phosphate biosynthetic process

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	0.98	intracellular part
GO:0044444	0.88	cytoplasmic part
GO:0043226	0.82	organelle
GO:0043227	0.78	membrane-bounded organelle
GO:0043229	0.73	intracellular organelle
GO:0043231	0.70	intracellular membrane-bounded organelle
GO:0044422	0.62	organelle part
GO:0044446	0.60	intracellular organelle 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	0.598	1akyA	0.866	1.49	0.581	0.908	2.7.4.3	28,142,175,177,178,186
2	0.578	3fb4A	0.850	1.49	0.414	0.900	2.7.4.3	28,48,142,165,175,177,178,186
3	0.506	1eckB	0.817	1.64	0.488	0.875	2.7.4.3	22,25,27,29,48,50,52,68,100,103,142,149,175,178
4	0.491	2qajB	0.854	1.51	0.384	0.904	2.7.4.3	25,27,29,43,48,52,71,74,103,142,144,175,177
5	0.491	1zioA	0.825	2.00	0.401	0.908	2.7.4.3	25,27,29,43,48,52,68,74,103,142,144,175,177

	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	0.73	2c9yA	0.716	3.81	0.838	0.862	1.43	B4P	complex1.pdb.gz	24,25,26,27,29,30,138,214,215,216
2	0.55	1e4yA	0.818	1.58	0.478	0.875	1.47	AP5	complex2.pdb.gz	24,25,26,27,28,29,30,46,47,51,72,73,74,79,100,103,107,138,142,152,153,156,157,175,186,214,216
3	0.41	4ukdA	0.718	2.09	0.283	0.791	1.34	UUU	complex3.pdb.gz	24,25,28,46,47,50,51,72,73,74,79,100,101,103,142,175,186
4	0.29	3l0sA	0.634	3.79	0.254	0.782	1.37	TAR	complex4.pdb.gz	23,24,25,26,27,28,142
5	0.28	3tlxA	0.880	1.53	0.454	0.925	1.52	AMP	complex5.pdb.gz	46,47,50,68,72,73,74,79,100,101,107,186
6	0.10	2axnA	0.604	4.31	0.101	0.803	0.83	EDT	complex6.pdb.gz	24,28,29,45,47,50,51,71,100,190
7	0.07	1zak0	0.815	2.18	0.359	0.904	1.30	III	complex7.pdb.gz	69,70,143,146,172,173,174,175,176,179,181,182
8	0.05	2bwj0	0.651	2.65	0.293	0.741	0.98	III	complex8.pdb.gz	46,47,103,141,186,189

	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.