D-I-TASSER O00408

D-I-TASSER results for O00408

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

Summary of the Protein

Uniprot ID: O00408
Protein Name: cGMP-dependent 3',5'-cyclic phosphodiesterase
Gene Name: PDE2A

Input Sequence in FASTA format

>O00408 (941 residues)
MGQACGHSILCRSQQYPAARPAEPRGQQVFLKPDEPPPPPQPCADSLQDALLSLGSVIDI
SGLQRAVKEALSAVLPRVETVYTYLLDGESQLVCEDPPHELPQEGKVREAIISQKRLGCN
GLGFSDLPGKPLARLVAPLAPDTQVLVMPLADKEAGAVAAVILVHCGQLSDNEEWSLQAV
EKHTLVALRRVQVLQQRGPREAPRAVQNPPEGTAEDQKGGAAYTDRDRKILQLCGELYDL
DASSLQLKVLQYLQQETRASRCCLLLVSEDNLQLSCKVIGDKVLGEEVSFPLTGCLGQVV
EDKKSIQLKDLTSEDVQQLQSMLGCELQAMLCVPVISRATDQVVALACAFNKLEGDLFTD
EDEHVIQHCFHYTSTVLTSTLAFQKEQKLKCECQALLQVAKNLFTHLDDVSVLLQEIITE
ARNLSNAEICSVFLLDQNELVAKVFDGGVVDDESYEIRIPADQGIAGHVATTGQILNIPD
AYAHPLFYRGVDDSTGFRTRNILCFPIKNENQEVIGVAELVNKINGPWFSKFDEDLATAF
SIYCGISIAHSLLYKKVNEAQYRSHLANEMMMYHMKVSDDEYTKLLHDGIQPVAAIDSNF
ASFTYTPRSLPEDDTSMAILSMLQDMNFINNYKIDCPTLARFCLMVKKGYRDPPYHNWMH
AFSVSHFCYLLYKNLELTNYLEDIEIFALFISCMCHDLDHRGTNNSFQVASKSVLAALYS
SEGSVMERHHFAQAIAILNTHGCNIFDHFSRKDYQRMLDLMRDIILATDLAHHLRIFKDL
QKMAEVGYDRNNKQHHRLLLCLLMTSCDLSDQTKGWKTTRKIAELIYKEFFSQGDLEKAM
GNRPMEMMDREKAYIPELQISFMEHIAMPIYKLLQDLFPKAAELYERVASNREHWTKVSH
KFTIRGLPSNNSLDFLDEEYEVPDLDGTRAPINGCCSLDAE

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 DeepPotential. 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	O00408-D1	1-201	201		MGQACGHSILCRSQQYPAARPAEPRGQQVFLKPDEPPPPPQPCADSLQDALLSLGSVIDISGLQRAVKEALSAVLPRVETVYTYLLDGESQLVCEDPPHELPQEGKVREAIISQKRLGCNGLGFSDLPGKPLARLVAPLAPDTQVLVMPLADKEAGAVAAVILVHCGQLSDNEEWSLQAVEKHTLVALRRVQVLQQRGPRE
2	O00408-D2	202-387	186		APRAVQNPPEGTAEDQKGGAAYTDRDRKILQLCGELYDLDASSLQLKVLQYLQQETRASRCCLLLVSEDNLQLSCKVIGDKVLGEEVSFPLTGCLGQVVEDKKSIQLKDLTSEDVQQLQSMLGCELQAMLCVPVISRATDQVVALACAFNKLEGDLFTDEDEHVIQHCFHYTSTVLTSTLAFQKEQ
3	O00408-D3	388-576	189		KLKCECQALLQVAKNLFTHLDDVSVLLQEIITEARNLSNAEICSVFLLDQNELVAKVFDGGVVDDESYEIRIPADQGIAGHVATTGQILNIPDAYAHPLFYRGVDDSTGFRTRNILCFPIKNENQEVIGVAELVNKINGPWFSKFDEDLATAFSIYCGISIAHSLLYKKVNEAQYRSHLANEMMMYHMK
4	O00408-D4	577-941	365		VSDDEYTKLLHDGIQPVAAIDSNFASFTYTPRSLPEDDTSMAILSMLQDMNFINNYKIDCPTLARFCLMVKKGYRDPPYHNWMHAFSVSHFCYLLYKNLELTNYLEDIEIFALFISCMCHDLDHRGTNNSFQVASKSVLAALYSSEGSVMERHHFAQAIAILNTHGCNIFDHFSRKDYQRMLDLMRDIILATDLAHHLRIFKDLQKMAEVGYDRNNKQHHRLLLCLLMTSCDLSDQTKGWKTTRKIAELIYKEFFSQGDLEKAMGNRPMEMMDREKAYIPELQISFMEHIAMPIYKLLQDLFPKAAELYERVASNREHWTKVSHKFTIRGLPSNNSLDFLDEEYEVPDLDGTRAPINGCCSLDAE

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.57

(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 DeepPotential, 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	7jsnA	0.47	6.07	0.159	0.585	model1_7jsnA.pdb.gz
2	6mzbB	0.46	6.20	0.153	0.585	model1_6mzbB.pdb.gz
3	3ibjA	0.37	6.01	0.463	0.468	model1_3ibjA.pdb.gz
4	4ehoA	0.35	4.81	0.067	0.408	model1_4ehoA.pdb.gz
5	5llwB	0.35	5.37	0.050	0.413	model1_5llwB.pdb.gz
6	2ouyA	0.34	1.59	0.341	0.347	model1_2ouyA.pdb.gz
7	3jsiA	0.34	1.26	0.254	0.341	model1_3jsiA.pdb.gz
8	1t9sA	0.34	1.35	0.332	0.342	model1_1t9sA.pdb.gz
9	2r8qA	0.34	1.85	0.286	0.345	model1_2r8qA.pdb.gz
10	4i15A	0.33	2.01	0.269	0.343	model1_4i15A.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	1.00	catalytic activity
GO:0004114	0.99	3',5'-cyclic-nucleotide phosphodiesterase activity
GO:1901363	0.81	heterocyclic compound binding
GO:0097159	0.81	organic cyclic compound binding
GO:0032555	0.74	purine ribonucleotide binding
GO:0030551	0.66	cyclic nucleotide binding
GO:0032561	0.60	guanyl ribonucleotide binding
GO:0004118	0.57	cGMP-stimulated cyclic-nucleotide phosphodiesterase activity
GO:0030553	0.54	cGMP 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:0044699	0.95	single-organism process
GO:0009987	0.95	cellular process
GO:0008152	0.91	metabolic process
GO:0044763	0.90	single-organism cellular process
GO:0071704	0.89	organic substance metabolic process
GO:0044238	0.89	primary metabolic process
GO:0034641	0.89	cellular nitrogen compound metabolic process
GO:0006139	0.88	nucleobase-containing compound metabolic process
GO:0044281	0.85	small molecule metabolic process
GO:0055086	0.84	nucleobase-containing small molecule metabolic process
GO:0009117	0.83	nucleotide metabolic process
GO:0065007	0.82	biological regulation
GO:0050789	0.82	regulation of biological process
GO:0009259	0.82	ribonucleotide metabolic process
GO:0006163	0.82	purine nucleotide metabolic process
GO:0009150	0.81	purine ribonucleotide metabolic process
GO:0050794	0.80	regulation of cellular process
GO:0009187	0.80	cyclic nucleotide metabolic process
GO:0007165	0.70	signal transduction
GO:0032501	0.69	multicellular organismal process
GO:0046068	0.68	cGMP metabolic process
GO:0050896	0.65	response to stimulus
GO:0046058	0.64	cAMP metabolic process
GO:0009214	0.64	cyclic nucleotide catabolic process
GO:0009154	0.64	purine ribonucleotide catabolic process
GO:0003008	0.63	system process
GO:0006198	0.59	cAMP catabolic process
GO:0065008	0.58	regulation of biological quality
GO:0042221	0.58	response to chemical
GO:0051716	0.57	cellular response to stimulus
GO:0048519	0.57	negative regulation of biological process
GO:1901700	0.56	response to oxygen-containing compound
GO:0035556	0.56	intracellular signal transduction
GO:0080090	0.55	regulation of primary metabolic process
GO:0048523	0.55	negative regulation of cellular process
GO:0046069	0.55	cGMP catabolic process
GO:0031323	0.55	regulation of cellular metabolic process
GO:0060255	0.54	regulation of macromolecule metabolic process
GO:0010033	0.54	response to organic substance
GO:0071310	0.53	cellular response to organic substance
GO:0019219	0.53	regulation of nucleobase-containing compound metabolic process
GO:1901701	0.52	cellular response to oxygen-containing compound
GO:0032879	0.52	regulation of localization
GO:0031326	0.52	regulation of cellular biosynthetic process
GO:0051049	0.51	regulation of transport
GO:0042493	0.51	response to drug
GO:0031324	0.51	negative regulation of cellular metabolic process
GO:0019933	0.51	cAMP-mediated signaling
GO:0010468	0.51	regulation of gene expression
GO:0035690	0.50	cellular response to drug
GO:0014070	0.50	response to organic cyclic compound
GO:0010243	0.50	response to organonitrogen compound

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	0.91	intracellular part
GO:0016020	0.83	membrane
GO:0043226	0.79	organelle
GO:0044444	0.76	cytoplasmic part
GO:0043229	0.76	intracellular organelle
GO:0043227	0.76	membrane-bounded organelle
GO:0043231	0.75	intracellular membrane-bounded organelle
GO:0005634	0.70	nucleus
GO:0005886	0.66	plasma membrane
GO:0048471	0.56	perinuclear region of cytoplasm
GO:0005829	0.53	cytosol

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	3b8eA	0.253	8.84	0.032	0.394	3.6.3.9	NA
2	0.060	1ynnJ	0.114	6.46	0.051	0.152	2.7.7.6	NA
3	0.060	1w36B	0.260	9.54	0.038	0.437	3.1.11.5	NA
4	0.060	1llwA	0.248	8.67	0.035	0.380	1.4.7.1	NA
5	0.060	1zklA	0.319	1.82	0.239	0.327	3.1.4.17	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

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, Qiqige Wuyun, Yang Li, Quancheng Liu, Xiaogen Zhou, Yiheng Zhu, P. Lydia Freddolino, Yang Zhang. Integrating deep learning potentials with I-TASSER for single- and multi-domain protein structure prediction. Submitted. 2023.