D-I-TASSER P10645

D-I-TASSER results for P10645

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

Summary of the Protein

Uniprot ID: P10645
Protein Name: Chromogranin-A
Gene Name: CHGA

Input Sequence in FASTA format

>P10645 (457 residues)
MRSAAVLALLLCAGQVTALPVNSPMNKGDTEVMKCIVEVISDTLSKPSPMPVSQECFETL
RGDERILSILRHQNLLKELQDLALQGAKERAHQQKKHSGFEDELSEVLENQSSQAELKEA
VEEPSSKDVMEKREDSKEAEKSGEATDGARPQALPEPMQESKAEGNNQAPGEEEEEEEEA
TNTHPPASLPSQKYPGPQAEGDSEGLSQGLVDREKGLSAEPGWQAKREEEEEEEEEAEAG
EEAVPEEEGPTVVLNPHPSLGYKEIRKGESRSEALAVDGAGKPGAEEAQDPEGKGEQEHS
QQKEEEEEMAVVPQGLFRGGKSGELEQEEERLSKEWEDSKRWSKMDQLAKELTAEKRLEG
QEEEEDNRDSSMKLSFRARAYGFRGPGPQLRRGWRPSSREDSLEAGLPLQVRGYPEEKKE
EEGSANRRPEDQELESLSAIEAELEKVAHQLQALRRG

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	P10645-D1	1-457	457		MRSAAVLALLLCAGQVTALPVNSPMNKGDTEVMKCIVEVISDTLSKPSPMPVSQECFETLRGDERILSILRHQNLLKELQDLALQGAKERAHQQKKHSGFEDELSEVLENQSSQAELKEAVEEPSSKDVMEKREDSKEAEKSGEATDGARPQALPEPMQESKAEGNNQAPGEEEEEEEEATNTHPPASLPSQKYPGPQAEGDSEGLSQGLVDREKGLSAEPGWQAKREEEEEEEEEAEAGEEAVPEEEGPTVVLNPHPSLGYKEIRKGESRSEALAVDGAGKPGAEEAQDPEGKGEQEHSQQKEEEEEMAVVPQGLFRGGKSGELEQEEERLSKEWEDSKRWSKMDQLAKELTAEKRLEGQEEEEDNRDSSMKLSFRARAYGFRGPGPQLRRGWRPSSREDSLEAGLPLQVRGYPEEKKEEEGSANRRPEDQELESLSAIEAELEKVAHQLQALRRG

Top 1 final models from D-I-TASSER

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Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.416

(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

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Top 10 structural analogs in PDB (as identified by TM-align)

Rank	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	Download Alignment
1	3qmzA	0.43	7.19	0.032	0.711	model1_3qmzA.pdb.gz
2	6z2wE	0.43	7.49	0.043	0.724	model1_6z2wE.pdb.gz
3	6vr4A	0.41	7.40	0.051	0.700	model1_6vr4A.pdb.gz
4	7dxjA	0.40	7.49	0.036	0.672	model1_7dxjA.pdb.gz
5	6g2dC	0.38	6.86	0.041	0.613	model1_6g2dC.pdb.gz
6	5i8iA	0.38	7.34	0.055	0.632	model1_5i8iA.pdb.gz
7	6sytA	0.37	7.58	0.041	0.654	model1_6sytA.pdb.gz
8	5yz0A	0.37	6.91	0.052	0.597	model1_5yz0A.pdb.gz
9	6jxaA	0.37	7.83	0.032	0.652	model1_6jxaA.pdb.gz
10	4gfhA	0.37	7.60	0.069	0.637	model1_4gfhA.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:1901363	0.57	heterocyclic compound binding
GO:0097159	0.57	organic cyclic compound binding
GO:0097367	0.52	carbohydrate derivative binding
GO:0000166	0.52	nucleotide binding
GO:0035639	0.51	purine ribonucleoside triphosphate binding
GO:0032555	0.51	purine ribonucleotide binding
GO:0032550	0.51	purine ribonucleoside binding
GO:0032559	0.50	adenyl ribonucleotide 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:0006887	1.00	exocytosis
GO:2000707	0.99	positive regulation of dense core granule biogenesis
GO:0050830	0.99	defense response to Gram-positive bacterium
GO:0050829	0.99	defense response to Gram-negative bacterium
GO:0043303	0.99	mast cell degranulation
GO:0033604	0.99	negative regulation of catecholamine secretion
GO:0032762	0.99	mast cell cytokine production
GO:0002551	0.99	mast cell chemotaxis
GO:0065008	0.69	regulation of biological quality
GO:0051239	0.68	regulation of multicellular organismal process
GO:0003008	0.68	system process
GO:0051241	0.67	negative regulation of multicellular organismal process
GO:0023051	0.67	regulation of signaling
GO:0010646	0.67	regulation of cell communication
GO:0080090	0.55	regulation of primary metabolic process
GO:0048522	0.55	positive regulation of cellular process
GO:0031323	0.55	regulation of cellular metabolic process
GO:0031325	0.53	positive regulation of cellular metabolic process
GO:0007165	0.53	signal transduction
GO:0019219	0.52	regulation of nucleobase-containing compound metabolic process
GO:0016043	0.52	cellular component organization
GO:0048583	0.51	regulation of response to stimulus
GO:0045935	0.51	positive regulation of nucleobase-containing compound metabolic process
GO:0019220	0.51	regulation of phosphate metabolic process
GO:0007186	0.51	G-protein coupled receptor signaling pathway
GO:0051240	0.50	positive regulation of multicellular organismal process
GO:0045937	0.50	positive regulation of phosphate metabolic process
GO:0009967	0.50	positive regulation of signal transduction
GO:0007187	0.50	G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger
GO:0006996	0.50	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:0044464	0.98	cell part
GO:0044424	0.97	intracellular part
GO:0044444	0.96	cytoplasmic part
GO:0043231	0.96	intracellular membrane-bounded organelle
GO:0030141	0.95	secretory granule
GO:0044421	0.72	extracellular region part
GO:0042583	0.70	chromaffin granule
GO:0005615	0.70	extracellular space
GO:0048471	0.50	perinuclear region of cytoplasm

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

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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	1b0pA	0.241	7.62	0.031	0.420	1.2.7.1	NA
2	0.060	3hkzJ	0.276	7.49	0.039	0.457	2.7.7.6	NA
3	0.060	2uv8G	0.333	7.41	0.026	0.558	2.3.1.86	NA
4	0.060	2vz9B	0.320	8.03	0.061	0.580	2.3.1.85	NA
5	0.060	2qtcB	0.279	6.97	0.031	0.444	1.2.4.1	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

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Template proteins with similar binding site:

No Binding sites was predicted

Click to view	Rank	Cscore^LB	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	BS-score	Lig. Name	Download Complex	Predicted binding site residues

	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.