D-I-TASSER P07992

D-I-TASSER results for P07992

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

Summary of the Protein

Uniprot ID: P07992
Protein Name: DNA excision repair protein ERCC-1
Gene Name: ERCC1

Input Sequence in FASTA format

>P07992 (297 residues)
MDPGKDKEGVPQPSGPPARKKFVIPLDEDEVPPGVAKPLFRSTQSLPTVDTSAQAAPQTY
AEYAISQPLEGAGATCPTGSEPLAGETPNQALKPGAKSNSIIVSPRQRGNPVLKFVRNVP
WEFGDVIPDYVLGQSTCALFLSLRYHNLHPDYIHGRLQSLGKNFALRVLLVQVDVKDPQQ
ALKELAKMCILADCTLILAWSPEEAGRYLETYKAYEQKPADLLMEKLEQDFVSRVTECLT
TVKSVNKTDSQTLLTTFGSLEQLIAASREDLALCPGLGPQKARRLFDVLHEPFLKVP

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	P07992-D1	1-297	297		MDPGKDKEGVPQPSGPPARKKFVIPLDEDEVPPGVAKPLFRSTQSLPTVDTSAQAAPQTYAEYAISQPLEGAGATCPTGSEPLAGETPNQALKPGAKSNSIIVSPRQRGNPVLKFVRNVPWEFGDVIPDYVLGQSTCALFLSLRYHNLHPDYIHGRLQSLGKNFALRVLLVQVDVKDPQQALKELAKMCILADCTLILAWSPEEAGRYLETYKAYEQKPADLLMEKLEQDFVSRVTECLTTVKSVNKTDSQTLLTTFGSLEQLIAASREDLALCPGLGPQKARRLFDVLHEPFLKVP

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.5709

(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	2bgwA	0.66	1.26	0.157	0.687	model1_2bgwA.pdb.gz
2	4bxoA	0.49	3.85	0.124	0.606	model1_4bxoA.pdb.gz
3	6hluA	0.48	5.97	0.072	0.771	model1_6hluA.pdb.gz
4	4xylA	0.45	5.60	0.079	0.680	model1_4xylA.pdb.gz
5	5wlcSI	0.45	5.19	0.068	0.670	model1_5wlcSI.pdb.gz
6	1t3tA	0.45	5.80	0.068	0.707	model1_1t3tA.pdb.gz
7	2o8fA	0.44	6.23	0.048	0.731	model1_2o8fA.pdb.gz
8	5owvA	0.43	5.25	0.055	0.633	model1_5owvA.pdb.gz
9	6bzfB	0.43	4.09	0.091	0.552	model1_6bzfB.pdb.gz
10	2zivA	0.43	3.33	0.080	0.505	model1_2zivA.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	0.98	catalytic activity
GO:0004520	0.96	endodeoxyribonuclease activity
GO:1901363	0.87	heterocyclic compound binding
GO:0097159	0.87	organic cyclic compound binding
GO:0000014	0.87	single-stranded DNA endodeoxyribonuclease activity
GO:0003677	0.76	DNA binding
GO:0003684	0.74	damaged DNA binding
GO:0003697	0.64	single-stranded DNA binding
GO:0043566	0.62	structure-specific DNA binding
GO:0008022	0.62	protein C-terminus 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	0.95	response to stimulus
GO:0090304	0.92	nucleic acid metabolic process
GO:0080090	0.89	regulation of primary metabolic process
GO:0031323	0.89	regulation of cellular metabolic process
GO:0006259	0.89	DNA metabolic process
GO:0060255	0.82	regulation of macromolecule metabolic process
GO:0019219	0.82	regulation of nucleobase-containing compound metabolic process
GO:0006950	0.81	response to stress
GO:0006310	0.76	DNA recombination
GO:0006296	0.75	nucleotide-excision repair, DNA incision, 5'-to lesion
GO:0051052	0.69	regulation of DNA metabolic process
GO:0031324	0.62	negative regulation of cellular metabolic process
GO:0006312	0.62	mitotic recombination
GO:0032205	0.55	negative regulation of telomere maintenance
GO:0006979	0.55	response to oxidative stress
GO:0006295	0.55	nucleotide-excision repair, DNA incision, 3'-to lesion
GO:0051716	0.52	cellular response to stimulus

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:0044446	0.93	intracellular organelle part
GO:0044428	0.92	nuclear part
GO:0043229	0.73	intracellular organelle
GO:0043234	0.66	protein complex
GO:0043232	0.53	intracellular non-membrane-bounded organelle
GO:0005654	0.52	nucleoplasm

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	0.060	2aw5B	0.397	6.56	0.058	0.694	1.1.1.40	NA
2	0.060	2fhcA	0.423	6.65	0.043	0.737	3.2.1.41	262
3	0.060	1l5jA	0.422	6.44	0.049	0.734	4.2.1.3	NA
4	0.060	1ox4B	0.396	6.38	0.078	0.653	4.1.3.-	NA
5	0.060	2veoB	0.414	6.67	0.089	0.727	3.1.1.3	260

	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	0.03	2bgwA	0.663	1.26	0.157	0.687	0.53	QNA	complex1.pdb.gz	194,275,276,278,280,281
2	0.01	2v0nA	0.423	5.75	0.047	0.657	0.50	C2E	complex2.pdb.gz	256,259,270,277
3	0.01	2wb4B	0.427	5.72	0.064	0.667	0.46	C2E	complex3.pdb.gz	269,270,273,274
4	0.01	1ea0A	0.401	6.84	0.032	0.734	0.54	F3S	complex4.pdb.gz	256,257,270,271,274
5	0.01	2vdcA	0.399	6.14	0.052	0.650	0.54	F3S	complex5.pdb.gz	256,257,270,271,274
6	0.01	1w25A	0.391	5.74	0.051	0.583	0.54	C2E	complex6.pdb.gz	269,272,278,279

	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.