D-I-TASSER Q8NCN4

D-I-TASSER results for Q8NCN4

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

Summary of the Protein

Uniprot ID: Q8NCN4
Protein Name: E3 ubiquitin-protein ligase RNF169
Gene Name: RNF169

Input Sequence in FASTA format

>Q8NCN4 (708 residues)
MAAAGPSTRASSAAAAAALSRRGRRGRCDETAAAKTGAPGPASGPSLLVLSPPLLQPPLP
PRPEESGCAGCLEPPGEAAALPCGHSLCRGCAQRAADAAGPGCPRCRARGPGWARRRARD
DGQADSEVLGECARRSQPERCRPRRDGGAAAAGPRPEQEPRAAPAEPDFIFRAPIKLSKP
GELREEYESLRKLREEKLQEEKPSEDQIHKLLPEDTETGKRKMDEQKKRDEPLVLKTNLE
RCPARLSDSENEEPSRGQMTQTHRSAFVSKNNSYSLAFLAGKLNSKVERSQSCSDTAQER
AKSRVRAVPGNKAKVTTMTPASNPIIGVLLSTQNNRCVSAPDLTIEKRLPFSSLSSLASL
HKPERSVSPESNDSISEELNHFKPIVCSPCTPPKRLPDGRVLSPLIIKSTPRNLNRSLQK
QTSYEASPRILKKWEQIFQERQIKKTLSKATLTSLAPEMGEELLGSEGIHSSKEKPLVAV
NTRLSGGQVLSEYTGPTSADLDHFPSVSQTKAEQDSDNKSSTEIPLETCCSSELKGGGSG
TSLEREQFEGLGSTPDAKLDKTCISRAMKITTVNSVLPQNSVLGGVLKTKQQLKTLNHFD
LTNGVLVESLSEEPLPSLRRGRKRHCKTKHLEQNGSLKKLRQTSGEVGLAPTDPVLREME
QKLQQEEEDRQLALQLQRMFDNERRTVSRRKGSVDQYLLRSSNMAGAK

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	Q8NCN4-D1	1-708	708		MAAAGPSTRASSAAAAAALSRRGRRGRCDETAAAKTGAPGPASGPSLLVLSPPLLQPPLPPRPEESGCAGCLEPPGEAAALPCGHSLCRGCAQRAADAAGPGCPRCRARGPGWARRRARDDGQADSEVLGECARRSQPERCRPRRDGGAAAAGPRPEQEPRAAPAEPDFIFRAPIKLSKPGELREEYESLRKLREEKLQEEKPSEDQIHKLLPEDTETGKRKMDEQKKRDEPLVLKTNLERCPARLSDSENEEPSRGQMTQTHRSAFVSKNNSYSLAFLAGKLNSKVERSQSCSDTAQERAKSRVRAVPGNKAKVTTMTPASNPIIGVLLSTQNNRCVSAPDLTIEKRLPFSSLSSLASLHKPERSVSPESNDSISEELNHFKPIVCSPCTPPKRLPDGRVLSPLIIKSTPRNLNRSLQKQTSYEASPRILKKWEQIFQERQIKKTLSKATLTSLAPEMGEELLGSEGIHSSKEKPLVAVNTRLSGGQVLSEYTGPTSADLDHFPSVSQTKAEQDSDNKSSTEIPLETCCSSELKGGGSGTSLEREQFEGLGSTPDAKLDKTCISRAMKITTVNSVLPQNSVLGGVLKTKQQLKTLNHFDLTNGVLVESLSEEPLPSLRRGRKRHCKTKHLEQNGSLKKLRQTSGEVGLAPTDPVLREMEQKLQQEEEDRQLALQLQRMFDNERRTVSRRKGSVDQYLLRSSNMAGAK

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.5738

(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

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

Rank	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	Download Alignment
1	6yejA	0.31	8.64	0.031	0.515	model1_6yejA.pdb.gz
2	6um1A	0.31	7.80	0.050	0.487	model1_6um1A.pdb.gz
3	5nrlA	0.31	8.52	0.033	0.520	model1_5nrlA.pdb.gz
4	6wjvA	0.30	8.63	0.026	0.507	model1_6wjvA.pdb.gz
5	6mfzA	0.30	8.40	0.041	0.491	model1_6mfzA.pdb.gz
6	7cpxA	0.30	8.57	0.039	0.504	model1_7cpxA.pdb.gz
7	6sytA	0.30	8.01	0.043	0.469	model1_6sytA.pdb.gz
8	6ar6A	0.30	8.08	0.039	0.476	model1_6ar6A.pdb.gz
9	1vw1A	0.30	8.38	0.050	0.480	model1_1vw1A.pdb.gz
10	6jxaA	0.30	8.90	0.031	0.513	model1_6jxaA.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:0032182	0.93	ubiquitin-like protein binding
GO:0043130	0.92	ubiquitin binding
GO:0003682	0.92	chromatin binding
GO:0070530	0.91	K63-linked polyubiquitin binding
GO:0031491	0.80	nucleosome 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:0050794	0.98	regulation of cellular process
GO:0009987	0.98	cellular process
GO:0080090	0.96	regulation of primary metabolic process
GO:0031323	0.96	regulation of cellular metabolic process
GO:0060255	0.95	regulation of macromolecule metabolic process
GO:0050896	0.95	response to stimulus
GO:0048519	0.95	negative regulation of biological process
GO:0048523	0.94	negative regulation of cellular process
GO:0019219	0.94	regulation of nucleobase-containing compound metabolic process
GO:0006950	0.93	response to stress
GO:0048583	0.92	regulation of response to stimulus
GO:0031324	0.92	negative regulation of cellular metabolic process
GO:0010605	0.92	negative regulation of macromolecule metabolic process
GO:0080134	0.90	regulation of response to stress
GO:0045934	0.90	negative regulation of nucleobase-containing compound metabolic process
GO:0033554	0.90	cellular response to stress
GO:0006974	0.89	cellular response to DNA damage stimulus
GO:0006282	0.89	regulation of DNA repair
GO:0051053	0.75	negative regulation of DNA metabolic process
GO:2000780	0.74	negative regulation of double-strand break repair
GO:0008152	0.50	metabolic 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	0.96	intracellular organelle
GO:0044446	0.95	intracellular organelle part
GO:0005634	0.95	nucleus
GO:0035861	0.90	site of double-strand break
GO:0044428	0.85	nuclear part
GO:0005654	0.82	nucleoplasm

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	3ecqB	0.241	8.25	0.039	0.387	3.2.1.97	NA
2	0.060	2np0A	0.214	8.96	0.023	0.371	3.4.24.69	NA
3	0.060	1w36C	0.241	7.94	0.042	0.379	3.1.11.5	67
4	0.060	2vz9B	0.229	8.67	0.029	0.381	2.3.1.85	NA
5	0.060	2qf7A	0.279	7.25	0.032	0.411	6.4.1.1	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

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	2hdnA	0.039	2.18	0.031	0.041	0.44	GDP	complex1.pdb.gz	68,70,71,72,73
	2	0.01	2hcjB	0.133	6.88	0.071	0.192	0.42	TAC	complex2.pdb.gz	65,66,82,83,85

	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.