D-I-TASSER P0DJD9

D-I-TASSER results for P0DJD9

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

Summary of the Protein

Uniprot ID: P0DJD9
Protein Name: Pepsin A-5
Gene Name: PGA5

Input Sequence in FASTA format

>P0DJD9 (388 residues)
MKWLLLLGLVALSECIMYKVPLIRKKSLRRTLSERGLLKDFLKKHNLNPARKYFPQWEAP
TLVDEQPLENYLDMEYFGTIGIGTPAQDFTVVFDTGSSNLWVPSVYCSSLACTNHNRFNP
EDSSTYQSTSETVSITYGTGSMTGILGYDTVQVGGISDTNQIFGLSETEPGSFLYYAPFD
GILGLAYPSISSSGATPVFDNIWNQGLVSQDLFSVYLSADDKSGSVVIFGGIDSSYYTGS
LNWVPVTVEGYWQITVDSITMNGETIACAEGCQAIVDTGTSLLTGPTSPIANIQSDIGAS
ENSDGDMVVSCSAISSLPDIVFTINGVQYPVPPSAYILQSEGSCISGFQGMNVPTESGEL
WILGDVFIRQYFTVFDRANNQVGLAPVA

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	P0DJD9-D1	1-23,187-388	225		MKWLLLLGLVALSECIMYKVPLIYPSISSSGATPVFDNIWNQGLVSQDLFSVYLSADDKSGSVVIFGGIDSSYYTGSLNWVPVTVEGYWQITVDSITMNGETIACAEGCQAIVDTGTSLLTGPTSPIANIQSDIGASENSDGDMVVSCSAISSLPDIVFTINGVQYPVPPSAYILQSEGSCISGFQGMNVPTESGELWILGDVFIRQYFTVFDRANNQVGLAPVA
2	P0DJD9-D2	24-186	163		RKKSLRRTLSERGLLKDFLKKHNLNPARKYFPQWEAPTLVDEQPLENYLDMEYFGTIGIGTPAQDFTVVFDTGSSNLWVPSVYCSSLACTNHNRFNPEDSSTYQSTSETVSITYGTGSMTGILGYDTVQVGGISDTNQIFGLSETEPGSFLYYAPFDGILGLA

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.87

(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	0.89	2.18	0.808	0.949	model1_2psgA.pdb.gz
2	1qdmA	0.84	2.04	0.435	0.894	model1_1qdmA.pdb.gz
3	5ux4A	0.81	1.69	0.480	0.843	model1_5ux4A.pdb.gz
4	4aa8A	0.80	1.59	0.570	0.833	model1_4aa8A.pdb.gz
5	1dp5A	0.80	1.84	0.387	0.838	model1_1dp5A.pdb.gz
6	5mktA	0.80	1.81	0.394	0.838	model1_5mktA.pdb.gz
7	1tzsA	0.80	1.67	0.565	0.830	model1_1tzsA.pdb.gz
8	5n70A	0.80	2.08	0.440	0.840	model1_5n70A.pdb.gz
9	1am5A	0.79	1.85	0.596	0.835	model1_1am5A.pdb.gz
10	5nfgA	0.79	1.90	0.421	0.833	model1_5nfgA.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:0019538	0.98	protein metabolic process
GO:0006508	0.96	proteolysis
GO:0009057	0.94	macromolecule catabolic process
GO:0030163	0.93	protein catabolic process
GO:0009987	0.51	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	0.98	cell part
GO:0044424	0.95	intracellular part
GO:0043227	0.93	membrane-bounded organelle
GO:0044444	0.92	cytoplasmic part
GO:0043229	0.89	intracellular organelle
GO:0043231	0.88	intracellular membrane-bounded organelle
GO:0005773	0.76	vacuole
GO:0000323	0.62	lytic vacuole
GO:0044421	0.59	extracellular region part
GO:0005764	0.58	lysosome
GO:0005615	0.51	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	0.580	3psgA	0.873	2.07	0.814	0.928	3.4.23.1	94,95,137,277,278,280
2	0.558	1tzsA	0.796	1.67	0.565	0.830	3.4.23.34	94,95,97,137,277,278,280
3	0.546	1ibqA	0.744	2.24	0.321	0.804	3.4.23.18	94,95,97,137,277,278,280
4	0.502	1dp5A	0.797	1.84	0.387	0.838	3.4.23.25	94,95,97,274,277,137
5	0.493	1od1A	0.738	2.51	0.298	0.812	3.4.23.22	94,95,97,277,278,280

	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	0.90	1psoE	0.809	1.62	0.960	0.840	1.43	III	complex1.pdb.gz	74,94,96,97,136,137,173,251,277,279,280,281,349,353
2	0.84	1psaA	0.808	1.59	0.844	0.840	1.53	0ZL	complex2.pdb.gz	94,96,137,179,182,275,277,279,280,281,282,351,362
3	0.65	2bksB	0.785	1.96	0.381	0.833	1.23	PZ1	complex3.pdb.gz	74,75,76,94,96,101,103,115,142,166,169,179,180,181,182,277,279,281
4	0.64	2g1oA	0.785	1.94	0.381	0.833	1.01	2IG	complex4.pdb.gz	76,92,94,96,137,138,139,173,174,176,177,179,182,277,278,279,281
5	0.62	3oqkB	0.794	1.96	0.377	0.840	0.93	S52	complex5.pdb.gz	94,137,182,277,279,281
6	0.62	2g1sA	0.784	1.94	0.381	0.833	1.02	4IG	complex6.pdb.gz	74,75,76,92,94,96,137,182,277,278,279,281
7	0.49	3ownA	0.787	2.10	0.377	0.840	1.01	3OX	complex7.pdb.gz	75,94,96,136,137,138,174,176,277,279,280,281,282,284
8	0.42	3g6zA	0.791	2.06	0.377	0.840	0.85	A7T	complex8.pdb.gz	94,96,101,102,103,115,135,166,169,174,277
9	0.42	1psa0	0.808	1.59	0.844	0.840	1.56	III	complex9.pdb.gz	79,86,87,88,105,114,115,116,117,122,176,221,222,223
10	0.36	1dpjA	0.797	1.84	0.387	0.838	1.01	III	complex10.pdb.gz	94,182,190,192,248,250,251,277,280,282,306,338,340,341,343,349,351,353,357

	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.