D-I-TASSER P07339

D-I-TASSER results for P07339

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

Summary of the Protein

Uniprot ID: P07339
Protein Name: Cathepsin D
Gene Name: CTSD

Input Sequence in FASTA format

>P07339 (412 residues)
MQPSSLLPLALCLLAAPASALVRIPLHKFTSIRRTMSEVGGSVEDLIAKGPVSKYSQAVP
AVTEGPIPEVLKNYMDAQYYGEIGIGTPPQCFTVVFDTGSSNLWVPSIHCKLLDIACWIH
HKYNSDKSSTYVKNGTSFDIHYGSGSLSGYLSQDTVSVPCQSASSASALGGVKVERQVFG
EATKQPGITFIAAKFDGILGMAYPRISVNNVLPVFDNLMQQKLVDQNIFSFYLSRDPDAQ
PGGELMLGGTDSKYYKGSLSYLNVTRKAYWQVHLDQVEVASGLTLCKEGCEAIVDTGTSL
MVGPVDEVRELQKAIGAVPLIQGEYMIPCEKVSTLPAITLKLGGKGYKLSPEDYTLKVSQ
AGKTLCLSGFMGMDIPPPSGPLWILGDVFIGRYYTVFDRDNNRVGFAEAARL

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	P07339-D1	1-26,203-412	236		MQPSSLLPLALCLLAAPASALVRIPLYPRISVNNVLPVFDNLMQQKLVDQNIFSFYLSRDPDAQPGGELMLGGTDSKYYKGSLSYLNVTRKAYWQVHLDQVEVASGLTLCKEGCEAIVDTGTSLMVGPVDEVRELQKAIGAVPLIQGEYMIPCEKVSTLPAITLKLGGKGYKLSPEDYTLKVSQAGKTLCLSGFMGMDIPPPSGPLWILGDVFIGRYYTVFDRDNNRVGFAEAARL
2	P07339-D2	27-202	176		HKFTSIRRTMSEVGGSVEDLIAKGPVSKYSQAVPAVTEGPIPEVLKNYMDAQYYGEIGIGTPPQCFTVVFDTGSSNLWVPSIHCKLLDIACWIHHKYNSDKSSTYVKNGTSFDIHYGSGSLSGYLSQDTVSVPCQSASSASALGGVKVERQVFGEATKQPGITFIAAKFDGILGMA

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.86

(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	2psgA	0.78	2.80	0.447	0.862	model1_2psgA.pdb.gz
2	1qdmA	0.78	2.68	0.489	0.850	model1_1qdmA.pdb.gz
3	5ux4A	0.77	2.07	0.846	0.816	model1_5ux4A.pdb.gz
4	5n70A	0.75	2.18	0.520	0.803	model1_5n70A.pdb.gz
5	5nfgA	0.75	2.47	0.449	0.803	model1_5nfgA.pdb.gz
6	2v0zC	0.75	2.36	0.442	0.801	model1_2v0zC.pdb.gz
7	1dp5A	0.74	2.27	0.445	0.794	model1_1dp5A.pdb.gz
8	5mktA	0.74	2.24	0.462	0.794	model1_5mktA.pdb.gz
9	1tzsA	0.74	2.03	0.531	0.782	model1_1tzsA.pdb.gz
10	4aa8A	0.74	2.07	0.461	0.782	model1_4aa8A.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	0.98	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:0008152	0.98	metabolic process
GO:0019538	0.97	protein metabolic process
GO:0006508	0.95	proteolysis
GO:0009057	0.93	macromolecule catabolic process
GO:0030163	0.92	protein catabolic 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	0.98	cell part
GO:0044424	0.96	intracellular part
GO:0044444	0.94	cytoplasmic part
GO:0043227	0.94	membrane-bounded organelle
GO:0043231	0.91	intracellular membrane-bounded organelle
GO:0005773	0.81	vacuole
GO:0000323	0.69	lytic vacuole
GO:0005764	0.66	lysosome
GO:0044421	0.63	extracellular region part
GO:0005615	0.57	extracellular space

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	0.563	1flhA	0.746	2.02	0.475	0.789	3.4.23.1	97,98,100,142,295,296,298
2	0.533	1dp5A	0.742	2.16	0.445	0.791	3.4.23.25	142
3	0.528	1cmsA	0.739	2.09	0.461	0.782	3.4.23.4	97,98,100,142,295,296,298
4	0.512	1tzsA	0.741	2.03	0.531	0.782	3.4.23.34	97,98,100,142,295,296,298
5	0.509	1psnA	0.748	1.97	0.475	0.789	3.4.23.1	95,97,99,140,143,145,193,195,198,269,293,295,298,300

	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	0.72	2g20A	0.745	2.25	0.453	0.798	1.16	L1A	complex1.pdb.gz	78,97,99,142,143,189,190,192,193,195,198,295,297,298,299,300,302,371,373,384
2	0.70	3g72A	0.737	2.31	0.444	0.794	0.97	A6T	complex2.pdb.gz	78,97,99,104,105,106,120,140,142,182,185,189,190,193,195,196,198
3	0.70	3q3tA	0.748	2.21	0.445	0.798	1.05	RX0	complex3.pdb.gz	77,78,97,99,142,143,144,189,195,295,296,297,299
4	0.69	2g24A	0.742	2.21	0.453	0.794	1.03	7IG	complex4.pdb.gz	95,97,142,143,144,189,190,192,195,198,295
5	0.69	1psaA	0.750	1.96	0.488	0.791	0.88	0ZL	complex5.pdb.gz	97,99,142,293,297,298,299,300,373,384
6	0.56	2v12C	0.742	2.22	0.444	0.794	1.05	C39	complex6.pdb.gz	77,78,95,97,99,100,101,102,141,142,143,144,193,198,206,233,295,296,297,298
7	0.55	3oqfB	0.750	2.18	0.445	0.798	0.83	S51	complex7.pdb.gz	78,97,142,144,198
8	0.45	3o9lA	0.358	2.34	0.457	0.384	1.28	LPN	complex8.pdb.gz	79,95,97,104,105,120,147,182,185,190,195,196,198
9	0.34	1g0vA	0.743	2.13	0.445	0.791	1.27	III	complex9.pdb.gz	77,97,188,189,192,198,206,266,268,269,295,298,300,356,358,359,365,367,371,373,375,378,379
10	0.07	1g0vA	0.743	2.13	0.445	0.791	0.85	UUU	complex10.pdb.gz	134,176,178,209,210,211,212

	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.