D-I-TASSER P35354

D-I-TASSER results for P35354

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

Summary of the Protein

Uniprot ID: P35354
Protein Name: Prostaglandin G/H synthase 2
Gene Name: PTGS2

Input Sequence in FASTA format

>P35354 (604 residues)
MLARALLLCAVLALSHTANPCCSHPCQNRGVCMSVGFDQYKCDCTRTGFYGENCSTPEFL
TRIKLFLKPTPNTVHYILTHFKGFWNVVNNIPFLRNAIMSYVLTSRSHLIDSPPTYNADY
GYKSWEAFSNLSYYTRALPPVPDDCPTPLGVKGKKQLPDSNEIVEKLLLRRKFIPDPQGS
NMMFAFFAQHFTHQFFKTDHKRGPAFTNGLGHGVDLNHIYGETLARQRKLRLFKDGKMKY
QIIDGEMYPPTVKDTQAEMIYPPQVPEHLRFAVGQEVFGLVPGLMMYATIWLREHNRVCD
VLKQEHPEWGDEQLFQTSRLILIGETIKIVIEDYVQHLSGYHFKLKFDPELLFNKQFQYQ
NRIAAEFNTLYHWHPLLPDTFQIHDQKYNYQQFIYNNSILLEHGITQFVESFTRQIAGRV
AGGRNVPPAVQKVSQASIDQSRQMKYQSFNEYRKRFMLKPYESFEELTGEKEMSAELEAL
YGDIDAVELYPALLVEKPRPDAIFGETMVEVGAPFSLKGLMGNVICSPAYWKPSTFGGEV
GFQIINTASIQSLICNNVKGCPFTSFSVPDPELIKTVTINASSSRSGLDDINPTVLLKER
STEL

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	P35354-D1	1-67	67		MLARALLLCAVLALSHTANPCCSHPCQNRGVCMSVGFDQYKCDCTRTGFYGENCSTPEFLTRIKLFL
2	P35354-D2	68-135,173-420,497-604	424		KPTPNTVHYILTHFKGFWNVVNNIPFLRNAIMSYVLTSRSHLIDSPPTYNADYGYKSWEAFSNLSYYTFIPDPQGSNMMFAFFAQHFTHQFFKTDHKRGPAFTNGLGHGVDLNHIYGETLARQRKLRLFKDGKMKYQIIDGEMYPPTVKDTQAEMIYPPQVPEHLRFAVGQEVFGLVPGLMMYATIWLREHNRVCDVLKQEHPEWGDEQLFQTSRLILIGETIKIVIEDYVQHLSGYHFKLKFDPELLFNKQFQYQNRIAAEFNTLYHWHPLLPDTFQIHDQKYNYQQFIYNNSILLEHGITQFVESFTRQIAGRVKPRPDAIFGETMVEVGAPFSLKGLMGNVICSPAYWKPSTFGGEVGFQIINTASIQSLICNNVKGCPFTSFSVPDPELIKTVTINASSSRSGLDDINPTVLLKERSTEL
3	P35354-D3	136-172,421-496	113		RALPPVPDDCPTPLGVKGKKQLPDSNEIVEKLLLRRKAGGRNVPPAVQKVSQASIDQSRQMKYQSFNEYRKRFMLKPYESFEELTGEKEMSAELEALYGDIDAVELYPALLVE

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.931

(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	1cqeB	0.91	0.66	0.637	0.916	model1_1cqeB.pdb.gz
2	1cvuA	0.91	0.64	0.877	0.914	model1_1cvuA.pdb.gz
3	4hhrA	0.72	3.36	0.199	0.796	model1_4hhrA.pdb.gz
4	3faqA	0.65	3.77	0.147	0.733	model1_3faqA.pdb.gz
5	1mhlC	0.56	3.41	0.157	0.616	model1_1mhlC.pdb.gz
6	4k2bA	0.23	7.68	0.035	0.374	model1_4k2bA.pdb.gz
7	2hehA	0.18	7.41	0.044	0.281	model1_2hehA.pdb.gz
8	2dpnA1	0.16	6.50	0.066	0.238	model1_2dpnA1.pdb.gz
9	3es6A1	0.16	4.59	0.066	0.192	model1_3es6A1.pdb.gz
10	1tmxA2	0.15	6.66	0.025	0.222	model1_1tmxA2.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:0016491	0.98	oxidoreductase activity
GO:0004666	0.66	prostaglandin-endoperoxide synthase activity
GO:1901363	0.57	heterocyclic compound binding
GO:0097159	0.57	organic cyclic compound 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	0.93	single-organism process
GO:0009987	0.92	cellular process
GO:0065007	0.80	biological regulation
GO:0044763	0.79	single-organism cellular process
GO:0008152	0.76	metabolic process
GO:0044237	0.73	cellular metabolic process
GO:0071704	0.71	organic substance metabolic process
GO:0044710	0.68	single-organism metabolic process
GO:0044238	0.67	primary metabolic process
GO:0009058	0.65	biosynthetic process
GO:0050789	0.64	regulation of biological process
GO:0044281	0.64	small molecule metabolic process
GO:0044249	0.64	cellular biosynthetic process
GO:1901576	0.63	organic substance biosynthetic process
GO:0050896	0.62	response to stimulus
GO:0044711	0.62	single-organism biosynthetic process
GO:0006629	0.62	lipid metabolic process
GO:0006082	0.62	organic acid metabolic process
GO:0044255	0.61	cellular lipid metabolic process
GO:0019752	0.61	carboxylic acid metabolic process
GO:0016053	0.60	organic acid biosynthetic process
GO:0006631	0.60	fatty acid metabolic process
GO:0046394	0.59	carboxylic acid biosynthetic process
GO:0008610	0.59	lipid biosynthetic process
GO:0033559	0.58	unsaturated fatty acid metabolic process
GO:0006690	0.58	icosanoid metabolic process
GO:0050794	0.57	regulation of cellular process
GO:0001516	0.57	prostaglandin biosynthetic 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	0.94	intracellular part
GO:0043226	0.86	organelle
GO:0043227	0.85	membrane-bounded organelle
GO:0043229	0.84	intracellular organelle
GO:0043231	0.82	intracellular membrane-bounded organelle
GO:0005737	0.78	cytoplasm
GO:0005634	0.67	nucleus
GO:0044444	0.53	cytoplasmic part

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	0.285	1mhlC	0.556	3.41	0.157	0.616	1.11.1.7	210,215,230,292,296,316,319,324
2	0.240	1prhA	0.911	0.73	0.635	0.917	1.14.99.1	NA
3	0.229	1cvuA	0.909	0.64	0.877	0.914	1.14.99.1	188,192
4	0.169	5coxA	0.909	0.61	0.879	0.914	1.14.99.1	184,335,337,339,366,370,372,375,503,507,509,512,514
5	0.087	1cxpC	0.556	3.47	0.157	0.618	1.11.1.7	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:

Rank	Cscore^LB	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	BS-score	Lig. Name	Download Complex	Predicted binding site residues
1	0.75	3ntbA	0.912	0.43	0.882	0.914	1.60	T1N	complex1.pdb.gz	106,335,338,341,345,367,371,373,509,512,513,517
2	0.74	1cvuB	0.907	0.79	0.877	0.914	1.92	ACD	complex2.pdb.gz	103,106,191,331,334,335,339,341,367,371,373,504,512,513,516,520
3	0.67	6coxB	0.909	0.62	0.879	0.914	1.39	HEM	complex3.pdb.gz	185,189,193,196,197,198,200,281,368,371,372,373,374,377,440
4	0.64	3ln1C	0.910	0.53	0.882	0.914	1.71	CEL	complex4.pdb.gz	75,106,178,335,338,339,341,345,371,373,499,502,503,504,509,512,513,516,517
5	0.61	1ddxB	0.909	0.64	0.882	0.914	1.76	PGX	complex5.pdb.gz	191,192,195,196,214,334,335,338,370,371,373,509,512,513,516,519,520
6	0.53	1ht8B	0.907	0.70	0.639	0.912	1.62	34C	complex6.pdb.gz	102,106,335,339,341,373,504,509,512,513,516
7	0.51	1ebvA	0.907	0.69	0.639	0.912	1.31	SCL	complex7.pdb.gz	106,338,341,373,509,513,516,517
8	0.46	5cox0	0.909	0.61	0.879	0.914	1.91	III	complex8.pdb.gz	31,33,34,35,36,37,43,45,46,112,113,114,120,122,123,124,125,126,128,215,306,307,308,309,312,313,316,319,353,354,355,356,357,358,359,524,527,528,529,530,531,532,534,535,537,538
9	0.10	3n8vB	0.910	0.69	0.638	0.916	0.80	UUU	complex9.pdb.gz	126,130,132,133

	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.