D-I-TASSER P27695

D-I-TASSER results for P27695

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

Summary of the Protein

Uniprot ID: P27695
Protein Name: DNA-(apurinic or apyrimidinic site) lyase
Gene Name: APEX1

Input Sequence in FASTA format

>P27695 (318 residues)
MPKRGKKGAVAEDGDELRTEPEAKKSKTAAKKNDKEAAGEGPALYEDPPDQKTSPSGKPA
TLKICSWNVDGLRAWIKKKGLDWVKEEAPDILCLQETKCSENKLPAELQELPGLSHQYWS
APSDKEGYSGVGLLSRQCPLKVSYGIGDEEHDQEGRVIVAEFDSFVLVTAYVPNAGRGLV
RLEYRQRWDEAFRKFLKGLASRKPLVLCGDLNVAHEEIDLRNPKGNKKNAGFTPQERQGF
GELLQAVPLADSFRHLYPNTPYAYTFWTYMMNARSKNVGWRLDYFLLSHSLLPALCDSKI
RSKALGSDHCPITLYLAL

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	P27695-D1	1-318	318		MPKRGKKGAVAEDGDELRTEPEAKKSKTAAKKNDKEAAGEGPALYEDPPDQKTSPSGKPATLKICSWNVDGLRAWIKKKGLDWVKEEAPDILCLQETKCSENKLPAELQELPGLSHQYWSAPSDKEGYSGVGLLSRQCPLKVSYGIGDEEHDQEGRVIVAEFDSFVLVTAYVPNAGRGLVRLEYRQRWDEAFRKFLKGLASRKPLVLCGDLNVAHEEIDLRNPKGNKKNAGFTPQERQGFGELLQAVPLADSFRHLYPNTPYAYTFWTYMMNARSKNVGWRLDYFLLSHSLLPALCDSKIRSKALGSDHCPITLYLAL

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.906

(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	1dewB	0.87	0.90	0.996	0.877	model1_1dewB.pdb.gz
2	2j63A	0.79	2.48	0.312	0.852	model1_2j63A.pdb.gz
3	3fziA	0.78	1.27	0.412	0.802	model1_3fziA.pdb.gz
4	5cfeA	0.77	0.96	0.510	0.789	model1_5cfeA.pdb.gz
5	5j8nA	0.77	1.60	0.426	0.805	model1_5j8nA.pdb.gz
6	2jc5A	0.76	1.63	0.353	0.802	model1_2jc5A.pdb.gz
7	4f1rA	0.75	1.59	0.281	0.796	model1_4f1rA.pdb.gz
8	2jc4A	0.74	1.70	0.317	0.783	model1_2jc4A.pdb.gz
9	2voaA	0.74	1.76	0.317	0.783	model1_2voaA.pdb.gz
10	1akoA	0.74	1.86	0.260	0.786	model1_1akoA.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	0.99	catalytic activity
GO:0004536	0.96	deoxyribonuclease activity
GO:0004527	0.95	exonuclease activity
GO:0004520	0.94	endodeoxyribonuclease activity
GO:0008408	0.93	3'-5' exonuclease activity
GO:0003906	0.93	DNA-(apurinic or apyrimidinic site) lyase activity
GO:0016895	0.90	exodeoxyribonuclease activity, producing 5'-phosphomonoesters
GO:0008311	0.88	double-stranded DNA 3'-5' exodeoxyribonuclease 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:0006974	1.00	cellular response to DNA damage stimulus
GO:0006259	1.00	DNA metabolic process
GO:0006281	0.99	DNA repair
GO:0006284	0.92	base-excision repair

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:0005634	0.99	nucleus

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	0.574	2voaA	0.742	1.76	0.316	0.786	4.2.99.18	171,210,283,309
2	0.562	2jc4A	0.741	1.70	0.317	0.783	3.1.11.2	68,210,212,283,309
3	0.282	2o3hA	0.862	0.65	0.982	0.868	4.2.99.18	210,212,283,309
4	0.187	2jc5A	0.762	1.63	0.353	0.802	3.1.11.2	68,210,212,283,309
5	0.138	1akoA	0.738	1.86	0.260	0.786	3.1.11.2	68,210,212,283,309

	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	0.53	1de9B	0.859	0.78	0.996	0.868	1.45	QNA	complex1.pdb.gz	96,128,171
2	0.50	1dewA	0.868	0.67	0.996	0.874	1.97	QNA	complex2.pdb.gz	70,71,73,74,78,126,127,177,224,269,270,271
3	0.50	1de8A	0.863	0.51	0.993	0.868	2.01	UUU	complex3.pdb.gz	96,128,171,174,177,210,212,226,229,230,266,268,271,278,280,282,309
4	0.50	1de9B	0.859	0.78	0.996	0.868	1.95	QNA	complex4.pdb.gz	96,171,174,177,210,212,222,226,229,230,266,268,270,271,276,278,280,282,309
5	0.26	2isiC	0.853	0.53	1.000	0.859	0.85	MG	complex5.pdb.gz	68,70,96
6	0.24	3g0rA	0.774	1.26	0.406	0.799	1.43	QNA	complex6.pdb.gz	70,71,73,74,77,78,98,103,126,127,266,268,269,270,271,308
7	0.20	3ga6B	0.772	1.32	0.406	0.799	1.30	QNA	complex7.pdb.gz	96,125,128,171,210,212,309
8	0.06	2dnjA	0.593	2.69	0.167	0.676	0.89	QNA	complex8.pdb.gz	70,96,124,125,130,156,174

	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.