D-I-TASSER Q53GL7

D-I-TASSER results for Q53GL7

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

Summary of the Protein

Uniprot ID: Q53GL7
Protein Name: Protein mono-ADP-ribosyltransferase PARP10
Gene Name: PARP10

Input Sequence in FASTA format

>Q53GL7 (1025 residues)
MVAMAEAEAGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLGCGGVLTFREPA
DAERVLAQADHELHGAQLSLRPAPPRAPARLLLQGLPPGTTPQRLEQHVQALLRASGLPV
QPCCALASPRPDRALVQLPKPLSEADVRVLEEQAQNLGLEGTLVSLARVPQARAVRVVGD
GASVDLLLLELYLENERRSGGGPLEDLQRLPGPLGTVASFQQWQVAERVLQQEHRLQGSE
LSLVPHYDILEPEELAENTSGGDHPSTQGPRATKHALLRTGGLVTALQGAGTVTMGSGEE
PGQSGASLRTGPMVQGRGIMTTGSGQEPGQSGTSLRTGPMGSLGQAEQVSSMPMGSLEHE
GLVSLRPVGLQEQEGPMSLGPVGSAGPVETSKGLLGQEGLVEIAMDSPEQEGLVGPMEIT
MGSLEKAGPVSPGCVKLAGQEGLVEMVLLMEPGAMRFLQLYHEDLLAGLGDVALLPLEGP
DMTGFRLCGAQASCQAAEEFLRSLLGSISCHVLCLEHPGSARFLLGPEGQHLLQGLEAQF
QCVFGTERLATATLDTGLEEVDPTEALPVLPGNAHTLWTPDSTGGDQEDVSLEEVRELLA
TLEGLDLDGEDWLPRELEEEGPQEQPEEEVTPGHEEEEPVAPSTVAPRWLEEEAALQLAL
HRSLEPQGQVAEQEEAAALRQALTLSLLEQPPLEAEEPPDGGTDGKAQLVVHSAFEQDVE
ELDRALRAALEVHVQEETVGPWRRTLPAELRARLERCHGVSVALRGDCTILRGFGAHPAR
AARHLVALLAGPWDQSLAFPLAASGPTLAGQTLKGPWNNLERLAENTGEFQEVVRAFYDT
LDAARSSIRVVRVERVSHPLLQQQYELYRERLLQRCERRPVEQVLYHGTTAPAVPDICAH
GFNRSFCGRNATVYGKGVYFARRASLSVQDRYSPPNADGHKAVFVARVLTGDYGQGRRGL
RAPPLRGPGHVLLRYDSAVDCICQPSIFVIFHDTQALPTHLITCEHVPRASPDDPSGLPG
RSPDT

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	Q53GL7-D1	1-167,248-385	305		MVAMAEAEAGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLGCGGVLTFREPADAERVLAQADHELHGAQLSLRPAPPRAPARLLLQGLPPGTTPQRLEQHVQALLRASGLPVQPCCALASPRPDRALVQLPKPLSEADVRVLEEQAQNLGLEGTLVSLADILEPEELAENTSGGDHPSTQGPRATKHALLRTGGLVTALQGAGTVTMGSGEEPGQSGASLRTGPMVQGRGIMTTGSGQEPGQSGTSLRTGPMGSLGQAEQVSSMPMGSLEHEGLVSLRPVGLQEQEGPMSLGPVGSA
2	Q53GL7-D2	168-247,402-447,670-853	310		RVPQARAVRVVGDGASVDLLLLELYLENERRSGGGPLEDLQRLPGPLGTVASFQQWQVAERVLQQEHRLQGSELSLVPHYEIAMDSPEQEGLVGPMEITMGSLEKAGPVSPGCVKLAGQEGLVEMVVAEQEEAAALRQALTLSLLEQPPLEAEEPPDGGTDGKAQLVVHSAFEQDVEELDRALRAALEVHVQEETVGPWRRTLPAELRARLERCHGVSVALRGDCTILRGFGAHPARAARHLVALLAGPWDQSLAFPLAASGPTLAGQTLKGPWNNLERLAENTGEFQEVVRAFYDTLDAARSSIRVVRV
3	Q53GL7-D3	386-401,592-669	94		GPVETSKGLLGQEGLVLEEVRELLATLEGLDLDGEDWLPRELEEEGPQEQPEEEVTPGHEEEEPVAPSTVAPRWLEEEAALQLALHRSLEPQGQ
4	Q53GL7-D4	448-591,854-929	220		LLMEPGAMRFLQLYHEDLLAGLGDVALLPLEGPDMTGFRLCGAQASCQAAEEFLRSLLGSISCHVLCLEHPGSARFLLGPEGQHLLQGLEAQFQCVFGTERLATATLDTGLEEVDPTEALPVLPGNAHTLWTPDSTGGDQEDVSERVSHPLLQQQYELYRERLLQRCERRPVEQVLYHGTTAPAVPDICAHGFNRSFCGRNATVYGKGVYFARRASLSVQ
5	Q53GL7-D5	930-1025	96		DRYSPPNADGHKAVFVARVLTGDYGQGRRGLRAPPLRGPGHVLLRYDSAVDCICQPSIFVIFHDTQALPTHLITCEHVPRASPDDPSGLPGRSPDT

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.39

(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	1llwA	0.29	8.83	0.049	0.445	model1_1llwA.pdb.gz
2	2vdcA	0.28	8.70	0.049	0.433	model1_2vdcA.pdb.gz
3	1t3tA	0.28	9.54	0.055	0.461	model1_1t3tA.pdb.gz
4	6v85A	0.28	9.31	0.033	0.443	model1_6v85A.pdb.gz
5	5m59A	0.28	9.32	0.034	0.441	model1_5m59A.pdb.gz
6	6rc9A1	0.28	9.61	0.037	0.447	model1_6rc9A1.pdb.gz
7	5gm6B	0.27	9.17	0.041	0.429	model1_5gm6B.pdb.gz
8	2xvgA	0.27	9.52	0.031	0.436	model1_2xvgA.pdb.gz
9	5jouA	0.27	9.33	0.025	0.426	model1_5jouA.pdb.gz
10	4q2cA	0.27	8.68	0.062	0.407	model1_4q2cA.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:0016740	0.97	transferase activity
GO:0003950	0.96	NAD+ ADP-ribosyltransferase activity
GO:0070530	0.87	K63-linked polyubiquitin 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	0.99	cellular process
GO:0065007	0.98	biological regulation
GO:0050789	0.96	regulation of biological process
GO:0044699	0.95	single-organism process
GO:0050794	0.94	regulation of cellular process
GO:0044763	0.94	single-organism cellular process
GO:0044238	0.94	primary metabolic process
GO:0044237	0.94	cellular metabolic process
GO:0043170	0.94	macromolecule metabolic process
GO:0044260	0.93	cellular macromolecule metabolic process
GO:0080090	0.92	regulation of primary metabolic process
GO:0060255	0.92	regulation of macromolecule metabolic process
GO:0048519	0.92	negative regulation of biological process
GO:0019538	0.92	protein metabolic process
GO:0051246	0.91	regulation of protein metabolic process
GO:0044710	0.91	single-organism metabolic process
GO:0010468	0.91	regulation of gene expression
GO:0009892	0.91	negative regulation of metabolic process
GO:0006464	0.91	cellular protein modification process
GO:0031323	0.90	regulation of cellular metabolic process
GO:0010629	0.90	negative regulation of gene expression
GO:0006471	0.90	protein ADP-ribosylation
GO:0065009	0.89	regulation of molecular function
GO:0051128	0.89	regulation of cellular component organization
GO:0045071	0.89	negative regulation of viral genome replication
GO:0044087	0.89	regulation of cellular component biogenesis
GO:0031399	0.89	regulation of protein modification process
GO:0006355	0.89	regulation of transcription, DNA-templated
GO:1900045	0.88	negative regulation of protein K63-linked ubiquitination
GO:0070213	0.88	protein auto-ADP-ribosylation
GO:0070212	0.88	protein poly-ADP-ribosylation
GO:0048147	0.88	negative regulation of fibroblast proliferation
GO:0033159	0.88	negative regulation of protein import into nucleus, translocation
GO:0032088	0.88	negative regulation of NF-kappaB transcription factor activity
GO:0010847	0.88	regulation of chromatin assembly

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:0043231	0.97	intracellular membrane-bounded organelle
GO:0044444	0.96	cytoplasmic part
GO:0044428	0.96	nuclear part
GO:0005654	0.94	nucleoplasm
GO:0005794	0.92	Golgi apparatus
GO:0005634	0.70	nucleus
GO:0005737	0.67	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

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	3b9jJ	0.141	6.17	0.036	0.179	1.17.1.4 1.17.3.2	NA
2	0.060	1fo4A	0.242	9.78	0.039	0.402	1.17.1.4	NA
3	0.060	1t3tA	0.279	9.54	0.055	0.461	6.3.5.3	454,462
4	0.060	3b9jI	0.099	5.62	0.056	0.122	1.17.1.4 1.17.3.2	306
5	0.060	1mswD	0.235	8.45	0.049	0.353	2.7.7.6	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:

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
	1	0.01	2vdcA	0.284	8.70	0.049	0.433	0.44	F3S	complex1.pdb.gz	261,262,263,264,265,297
	2	0.01	1lm1A	0.292	9.38	0.049	0.468	0.44	F3S	complex2.pdb.gz	261,262,263,264,265,298

	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.