D-I-TASSER O43543

D-I-TASSER results for O43543

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

Summary of the Protein

Uniprot ID: O43543
Protein Name: DNA repair protein XRCC2
Gene Name: XRCC2

Input Sequence in FASTA format

>O43543 (280 residues)
MCSAFHRAESGTELLARLEGRSSLKEIEPNLFADEDSPVHGDILEFHGPEGTGKTEMLYH
LTARCILPKSEGGLEVEVLFIDTDYHFDMLRLVTILEHRLSQSSEEIIKYCLGRFFLVYC
SSSTHLLLTLYSLESMFCSHPSLCLLILDSLSAFYWIDRVNGGESVNLQESTLRKCSQCL
EKLVNDYRLVLFATTQTIMQKASSSSEEPSHASRRLCDVDIDYRPYLCKAWQQLVKHRMF
FSKQDDSQSSNQFSLVSRCLKSNSLKKHFFIIGESGVEFC

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	O43543-D1	1-280	280		MCSAFHRAESGTELLARLEGRSSLKEIEPNLFADEDSPVHGDILEFHGPEGTGKTEMLYHLTARCILPKSEGGLEVEVLFIDTDYHFDMLRLVTILEHRLSQSSEEIIKYCLGRFFLVYCSSSTHLLLTLYSLESMFCSHPSLCLLILDSLSAFYWIDRVNGGESVNLQESTLRKCSQCLEKLVNDYRLVLFATTQTIMQKASSSSEEPSHASRRLCDVDIDYRPYLCKAWQQLVKHRMFFSKQDDSQSSNQFSLVSRCLKSNSLKKHFFIIGESGVEFC

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.8119

(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	1xu4A	0.85	1.83	0.163	0.900	model1_1xu4A.pdb.gz
2	7c9aA	0.82	2.46	0.220	0.893	model1_7c9aA.pdb.gz
3	2zucB	0.77	2.04	0.174	0.829	model1_2zucB.pdb.gz
4	1szpA	0.77	2.21	0.222	0.836	model1_1szpA.pdb.gz
5	2zjbA	0.77	2.16	0.206	0.832	model1_2zjbA.pdb.gz
6	1pznA	0.75	2.47	0.228	0.829	model1_1pznA.pdb.gz
7	3cmuA	0.73	3.14	0.142	0.854	model1_3cmuA.pdb.gz
8	4nmnA2	0.73	3.69	0.088	0.882	model1_4nmnA2.pdb.gz
9	4zc0A	0.72	3.62	0.117	0.871	model1_4zc0A.pdb.gz
10	3bgwA	0.72	3.79	0.089	0.871	model1_3bgwA.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	1.00	catalytic activity
GO:0003676	1.00	nucleic acid binding
GO:0016887	0.99	ATPase activity
GO:0003697	0.99	single-stranded DNA binding
GO:0003690	0.99	double-stranded DNA binding
GO:0000150	0.98	recombinase activity
GO:0008094	0.94	DNA-dependent ATPase activity
GO:0016788	0.93	hydrolase activity, acting on ester bonds
GO:0004520	0.92	endodeoxyribonuclease activity
GO:0000400	0.92	four-way junction DNA 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:0050896	1.00	response to stimulus
GO:0006259	1.00	DNA metabolic process
GO:0016043	0.99	cellular component organization
GO:0006310	0.99	DNA recombination
GO:0000730	0.98	DNA recombinase assembly
GO:0022402	0.97	cell cycle process
GO:0010212	0.97	response to ionizing radiation
GO:1903046	0.96	meiotic cell cycle process
GO:0042148	0.96	strand invasion
GO:0006312	0.96	mitotic recombination
GO:0007131	0.94	reciprocal meiotic recombination
GO:0006996	0.55	organelle organization

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:0044428	1.00	nuclear part
GO:0043226	0.68	organelle
GO:0043229	0.67	intracellular organelle
GO:0032991	0.62	macromolecular complex
GO:0043234	0.59	protein complex
GO:0044427	0.57	chromosomal part
GO:0043232	0.57	intracellular non-membrane-bounded organelle
GO:0033061	0.53	DNA recombinase mediator complex
GO:0005654	0.53	nucleoplasm
GO:0033063	0.52	Rad51B-Rad51C-Rad51D-XRCC2 complex
GO:0005657	0.52	replication fork

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	0.228	1g64B	0.452	3.31	0.118	0.539	2.5.1.17	54
2	0.066	1cbuB	0.454	3.50	0.089	0.564	2.7.1.156 2.7.7.62	NA
3	0.060	3mmtA	0.470	5.63	0.055	0.714	4.1.2.13	NA
4	0.060	3mbfA	0.478	5.58	0.093	0.729	4.1.2.13	49
5	0.060	1vcnA	0.477	4.77	0.062	0.689	6.3.4.2	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	0.62	2i1qA	0.822	1.83	0.171	0.875	1.29	ANP	complex1.pdb.gz	50,51,52,53,54,55,56,84,91,94,272,273,274
2	0.30	2zrcA	0.688	2.95	0.152	0.793	1.39	PO4	complex2.pdb.gz	49,51,52,53,54,55
3	0.20	1cr4A	0.661	2.95	0.114	0.764	1.02	TYD	complex3.pdb.gz	48,51,52,53,54,55,56,196,243,272

	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.