D-I-TASSER P56817

D-I-TASSER results for P56817

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

Summary of the Protein

Uniprot ID: P56817
Protein Name: Beta-secretase 1
Gene Name: BACE1

Input Sequence in FASTA format

>P56817 (501 residues)
MAQALPWLLLWMGAGVLPAHGTQHGIRLPLRSGLGGAPLGLRLPRETDEEPEEPGRRGSF
VEMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGAAPHPFLHRYYQRQLSST
YRDLRKGVYVPYTQGKWEGELGTDLVSIPHGPNVTVRANIAAITESDKFFINGSNWEGIL
GLAYAEIARPDDSLEPFFDSLVKQTHVPNLFSLQLCGAGFPLNQSEVLASVGGSMIIGGI
DHSLYTGSLWYTPIRREWYYEVIIVRVEINGQDLKMDCKEYNYDKSIVDSGTTNLRLPKK
VFEAAVKSIKAASSTEKFPDGFWLGEQLVCWQAGTTPWNIFPVISLYLMGEVTNQSFRIT
ILPQQYLRPVEDVATSQDDCYKFAISQSSTGTVMGAVIMEGFYVVFDRARKRIGFAVSAC
HVHDEFRTAAVEGPFVTLDMEDCGYNIPQTDESTLMTIAYVMAAICALFMLPLCLMVCQW
RCLRCLRQQHDDFADDISLLK

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	P56817-D1	1-30,184-501	348		MAQALPWLLLWMGAGVLPAHGTQHGIRLPLYAEIARPDDSLEPFFDSLVKQTHVPNLFSLQLCGAGFPLNQSEVLASVGGSMIIGGIDHSLYTGSLWYTPIRREWYYEVIIVRVEINGQDLKMDCKEYNYDKSIVDSGTTNLRLPKKVFEAAVKSIKAASSTEKFPDGFWLGEQLVCWQAGTTPWNIFPVISLYLMGEVTNQSFRITILPQQYLRPVEDVATSQDDCYKFAISQSSTGTVMGAVIMEGFYVVFDRARKRIGFAVSACHVHDEFRTAAVEGPFVTLDMEDCGYNIPQTDESTLMTIAYVMAAICALFMLPLCLMVCQWRCLRCLRQQHDDFADDISLLK
2	P56817-D2	31-183	153		RSGLGGAPLGLRLPRETDEEPEEPGRRGSFVEMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGAAPHPFLHRYYQRQLSSTYRDLRKGVYVPYTQGKWEGELGTDLVSIPHGPNVTVRANIAAITESDKFFINGSNWEGILGLA

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.81

(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	3l58A	0.76	1.34	0.995	0.784	model1_3l58A.pdb.gz
2	2ewyA	0.71	1.78	0.550	0.745	model1_2ewyA.pdb.gz
3	1mppA	0.61	2.66	0.219	0.667	model1_1mppA.pdb.gz
4	5ux4A	0.59	2.53	0.283	0.643	model1_5ux4A.pdb.gz
5	5nfgA	0.59	2.60	0.252	0.641	model1_5nfgA.pdb.gz
6	4zl4A	0.59	2.88	0.196	0.647	model1_4zl4A.pdb.gz
7	6r5hA	0.59	3.13	0.215	0.657	model1_6r5hA.pdb.gz
8	4aa8A	0.59	2.36	0.251	0.629	model1_4aa8A.pdb.gz
9	1dp5A	0.58	2.68	0.252	0.633	model1_1dp5A.pdb.gz
10	1uh8A	0.58	2.64	0.217	0.635	model1_1uh8A.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:0004175	1.00	endopeptidase activity
GO:0004190	0.99	aspartic-type endopeptidase 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:0044238	0.97	primary metabolic process
GO:0043170	0.97	macromolecule metabolic process
GO:0019538	0.96	protein metabolic process
GO:0006508	0.95	proteolysis
GO:0030163	0.93	protein catabolic process
GO:0065007	0.59	biological regulation
GO:0050794	0.57	regulation of cellular 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	0.99	cell part
GO:0044424	0.96	intracellular part
GO:0044444	0.95	cytoplasmic part
GO:0043227	0.94	membrane-bounded organelle
GO:0043231	0.93	intracellular membrane-bounded organelle
GO:0005773	0.59	vacuole

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	0.629	3l58A	0.765	1.34	0.995	0.784	3.4.23.46	70,72,74,91,95,133,135,169,174,287,289,292,294,296,368,400
2	0.571	2zjiA	0.715	1.47	0.989	0.737	3.4.23.46	93,94,96,132,289,290,292
3	0.499	2qk5A	0.764	1.35	0.995	0.784	3.4.23.46	93,94,96,132,289,290,292
4	0.395	1flhA	0.584	2.41	0.261	0.627	3.4.23.1	93,94,96,132,289,292
5	0.378	1dp5A	0.583	2.68	0.252	0.633	3.4.23.25	132

	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	0.94	3skgB	0.752	1.27	1.000	0.770	1.80	PB8	complex1.pdb.gz	72,73,74,93,95,96,132,133,134,169,171,176,259,289,291,292,293,296
2	0.93	2ohuA	0.728	1.55	0.992	0.752	1.67	IP7	complex2.pdb.gz	73,74,93,95,96,130,137,169,171,176,189,289,291
3	0.93	3l5dB	0.756	1.39	0.997	0.776	1.59	BDV	complex3.pdb.gz	72,73,74,91,93,95,289,291,292,293
4	0.93	3i25A	0.724	1.41	0.997	0.745	1.73	MV7	complex4.pdb.gz	72,73,74,91,93,95,96,130,131,132,133,134,135,169,179,187,259,287,289,290,291,292,293,294,296,386,390,393,396
5	0.93	2q15A	0.744	1.51	0.990	0.768	1.54	3MR	complex5.pdb.gz	91,93,96,130,136,137,168,176,179,259,289,291,296,390
6	0.93	2zjkC	0.721	1.46	0.997	0.741	1.70	F1K	complex6.pdb.gz	72,91,132,133,171,179,291,292,293,296
7	0.93	3iviA	0.731	1.76	0.992	0.758	1.79	2LI	complex7.pdb.gz	91,93,95,96,130,131,132,133,169,179,259,285,287,289,291,292,390,393
8	0.93	2zjiA	0.715	1.47	0.989	0.737	1.46	F1I	complex8.pdb.gz	91,93,95,137,169,179,287,289,291,296,390,393
9	0.93	3hvgA	0.737	1.41	0.992	0.756	1.29	EV0	complex9.pdb.gz	91,93,95,132,133,134,169,176,289
10	0.92	2va5A	0.728	1.54	0.992	0.752	1.35	C8C	complex10.pdb.gz	72,91,93,171,179,289,291

	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.