D-I-TASSER Q96EB6

D-I-TASSER results for Q96EB6

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

Summary of the Protein

Uniprot ID: Q96EB6
Protein Name: NAD-dependent protein deacetylase sirtuin-1
Gene Name: SIRT1

Input Sequence in FASTA format

>Q96EB6 (747 residues)
MADEAALALQPGGSPSAAGADREAASSPAGEPLRKRPRRDGPGLERSPGEPGGAAPEREV
PAAARGCPGAAAAALWREAEAEAAAAGGEQEAQATAAAGEGDNGPGLQGPSREPPLADNL
YDEDDDDEGEEEEEAAAAAIGYRDNLLFGDEIITNGFHSCESDEEDRASHASSSDWTPRP
RIGPYTFVQQHLMIGTDPRTILKDLLPETIPPPELDDMTLWQIVINILSEPPKRKKRKDI
NTIEDAVKLLQECKKIIVLTGAGVSVSCGIPDFRSRDGIYARLAVDFPDLPDPQAMFDIE
YFRKDPRPFFKFAKEIYPGQFQPSLCHKFIALSDKEGKLLRNYTQNIDTLEQVAGIQRII
QCHGSFATASCLICKYKVDCEAVRGDIFNQVVPRCPRCPADEPLAIMKPEIVFFGENLPE
QFHRAMKYDKDEVDLLIVIGSSLKVRPVALIPSSIPHEVPQILINREPLPHLHFDVELLG
DCDVIINELCHRLGGEYAKLCCNPVKLSEITEKPPRTQKELAYLSELPPTPLHVSEDSSS
PERTSPPDSSVIVTLLDQAAKSNDDLDVSESKGCMEEKPQEVQTSRNVESIAEQMENPDL
KNVGSSTGEKNERTSVAGTVRKCWPNRVAKEQISRRLDGNQYLFLPPNRYIFHGAEVYSD
SEDDVLSSSSCGSNSDSGTCQSPSLEEPMEDESEIEEFYNGLEDEPDVPERAGGAGFGTD
GDDQEAINEAISVKQEVTDMNYPSNKS

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	Q96EB6-D1	1-747	747		MADEAALALQPGGSPSAAGADREAASSPAGEPLRKRPRRDGPGLERSPGEPGGAAPEREVPAAARGCPGAAAAALWREAEAEAAAAGGEQEAQATAAAGEGDNGPGLQGPSREPPLADNLYDEDDDDEGEEEEEAAAAAIGYRDNLLFGDEIITNGFHSCESDEEDRASHASSSDWTPRPRIGPYTFVQQHLMIGTDPRTILKDLLPETIPPPELDDMTLWQIVINILSEPPKRKKRKDINTIEDAVKLLQECKKIIVLTGAGVSVSCGIPDFRSRDGIYARLAVDFPDLPDPQAMFDIEYFRKDPRPFFKFAKEIYPGQFQPSLCHKFIALSDKEGKLLRNYTQNIDTLEQVAGIQRIIQCHGSFATASCLICKYKVDCEAVRGDIFNQVVPRCPRCPADEPLAIMKPEIVFFGENLPEQFHRAMKYDKDEVDLLIVIGSSLKVRPVALIPSSIPHEVPQILINREPLPHLHFDVELLGDCDVIINELCHRLGGEYAKLCCNPVKLSEITEKPPRTQKELAYLSELPPTPLHVSEDSSSPERTSPPDSSVIVTLLDQAAKSNDDLDVSESKGCMEEKPQEVQTSRNVESIAEQMENPDLKNVGSSTGEKNERTSVAGTVRKCWPNRVAKEQISRRLDGNQYLFLPPNRYIFHGAEVYSDSEDDVLSSSSCGSNSDSGTCQSPSLEEPMEDESEIEEFYNGLEDEPDVPERAGGAGFGTDGDDQEAINEAISVKQEVTDMNYPSNKS

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.639

(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	2hjhA	0.37	2.44	0.394	0.392	model1_2hjhA.pdb.gz
2	4i5iA	0.34	1.86	0.971	0.356	model1_4i5iA.pdb.gz
3	5ol0A	0.33	2.28	0.379	0.351	model1_5ol0A.pdb.gz
4	3gluA	0.33	1.92	0.385	0.343	model1_3gluA.pdb.gz
5	1q17C	0.33	2.63	0.352	0.348	model1_1q17C.pdb.gz
6	1j8fA	0.32	3.14	0.389	0.353	model1_1j8fA.pdb.gz
7	1iciA	0.31	2.56	0.275	0.329	model1_1iciA.pdb.gz
8	2h59A	0.31	2.31	0.339	0.324	model1_2h59A.pdb.gz
9	3jwpA	0.30	2.94	0.253	0.328	model1_3jwpA.pdb.gz
10	1s7gA	0.30	3.05	0.280	0.325	model1_1s7gA.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	0.80	catalytic activity
GO:0016787	0.76	hydrolase activity
GO:0016811	0.67	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides
GO:0019213	0.64	deacetylase activity
GO:0033558	0.59	protein deacetylase activity
GO:0034979	0.54	NAD-dependent protein deacetylase activity
GO:0004407	0.53	histone deacetylase activity
GO:0019899	0.50	enzyme 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:0009987	0.98	cellular process
GO:0065007	0.92	biological regulation
GO:0050789	0.92	regulation of biological process
GO:0050794	0.91	regulation of cellular process
GO:0019222	0.84	regulation of metabolic process
GO:0031323	0.83	regulation of cellular metabolic process
GO:0009889	0.77	regulation of biosynthetic process
GO:0080090	0.76	regulation of primary metabolic process
GO:0048519	0.76	negative regulation of biological process
GO:0031326	0.76	regulation of cellular biosynthetic process
GO:0060255	0.75	regulation of macromolecule metabolic process
GO:0048523	0.75	negative regulation of cellular process
GO:0008152	0.75	metabolic process
GO:0016043	0.74	cellular component organization
GO:0009892	0.74	negative regulation of metabolic process
GO:0071704	0.73	organic substance metabolic process
GO:0044699	0.73	single-organism process
GO:0044237	0.73	cellular metabolic process
GO:0031324	0.73	negative regulation of cellular metabolic process
GO:0044238	0.72	primary metabolic process
GO:0044260	0.71	cellular macromolecule metabolic process
GO:0010605	0.70	negative regulation of macromolecule metabolic process
GO:0051171	0.65	regulation of nitrogen compound metabolic process
GO:0010468	0.65	regulation of gene expression
GO:0048518	0.64	positive regulation of biological process
GO:0044763	0.63	single-organism cellular process
GO:0019219	0.63	regulation of nucleobase-containing compound metabolic process
GO:0006464	0.63	cellular protein modification process
GO:0010629	0.61	negative regulation of gene expression
GO:0035601	0.60	protein deacylation
GO:0048522	0.59	positive regulation of cellular process
GO:0032268	0.58	regulation of cellular protein metabolic process
GO:0006476	0.58	protein deacetylation
GO:0031399	0.55	regulation of protein modification process
GO:0009893	0.55	positive regulation of metabolic process
GO:0051239	0.54	regulation of multicellular organismal process
GO:0009891	0.54	positive regulation of biosynthetic process
GO:2000026	0.53	regulation of multicellular organismal development
GO:0051248	0.53	negative regulation of protein metabolic process
GO:0048583	0.53	regulation of response to stimulus
GO:0042981	0.53	regulation of apoptotic process
GO:0031325	0.53	positive regulation of cellular metabolic process
GO:0010604	0.53	positive regulation of macromolecule metabolic process
GO:0032269	0.52	negative regulation of cellular protein metabolic process
GO:0006325	0.52	chromatin organization
GO:0031328	0.51	positive regulation of cellular biosynthetic process
GO:0065008	0.50	regulation of biological quality
GO:0031400	0.50	negative regulation of protein modification 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:0044424	1.00	intracellular part
GO:0043229	0.98	intracellular organelle
GO:0043231	0.97	intracellular membrane-bounded organelle
GO:0005634	0.81	nucleus
GO:0044444	0.68	cytoplasmic part
GO:0005737	0.65	cytoplasm
GO:0044422	0.63	organelle part
GO:0044446	0.62	intracellular organelle 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	0.060	1l5jA	0.243	7.55	0.045	0.357	4.2.1.3	246,648
2	0.060	3b8eC	0.267	6.89	0.037	0.368	3.6.3.9	257
3	0.060	3k35F	0.263	3.88	0.183	0.294	2.4.2.31	NA
4	0.060	1kqfA	0.238	8.11	0.022	0.378	1.2.1.2	NA
5	0.060	1qbaA	0.245	8.27	0.034	0.386	3.2.1.52	260,267

	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	0.59	2hjhA	0.380	2.45	0.393	0.400	1.13	XYQ	complex1.pdb.gz	261,262,263,266,272,273,274,345,363,440,441,442,445,465,466,467,480,481,482
2	0.11	3gltA	0.331	1.79	0.394	0.341	1.23	III	complex2.pdb.gz	261,262,263,266,272,273,297,345,363,411,412,413,414,415,416,417,418,440,441,442,444,445,446,447,465,466,480
3	0.04	2h4hA	0.296	2.16	0.330	0.311	0.98	III	complex3.pdb.gz	297,363,412,414,415,416,417,418,444,445,446

	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.